#!/usr/bin/env bash
# Bulk download script for GSE80039
# Generated from Yeo Lab Publications Database
# Total files: 213

OUTDIR="GSE80039"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80039/suppl/GSE80039_RAW.tar" -O "GSE80039_RAW.tar"

# --- SRA run files ---
# Tip: use 'fasterq-dump' from SRA Toolkit for FASTQ conversion
#      with optional renaming to original submitted FASTQ names.
# Set to 1 to rename SRR outputs (e.g. SRR_1.fastq.gz -> sample_R1.fastq.gz)
RENAME_SRA_TO_ORIGINAL=1

_compress_if_exists() {
  local stem="$1"
  if [ -f "${stem}.fastq" ]; then
    gzip -f "${stem}.fastq"
    echo "${stem}.fastq.gz"
    return 0
  fi
  if [ -f "${stem}.fq" ]; then
    gzip -f "${stem}.fq"
    echo "${stem}.fq.gz"
    return 0
  fi
  return 1
}

# Option A: Download via SRA Toolkit (recommended)
fasterq-dump --split-files "SRR3346257"
gz1="$(_compress_if_exists 'SRR3346257_1' || true)"
gz2="$(_compress_if_exists 'SRR3346257_2' || true)"
gzs="$(_compress_if_exists 'SRR3346257' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "311_CLIP_ATTCAGAA-ATAGAGGC_L001_R1.A01_311_01_XRCC6.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "311_CLIP_ATTCAGAA-ATAGAGGC_L001_R2.A01_311_01_XRCC6.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346258"
gz1="$(_compress_if_exists 'SRR3346258_1' || true)"
gz2="$(_compress_if_exists 'SRR3346258_2' || true)"
gzs="$(_compress_if_exists 'SRR3346258' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "311_CLIP_ATTCAGAA-ATAGAGGC_L001_R1.B06_311_01_XRCC6.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "311_CLIP_ATTCAGAA-ATAGAGGC_L001_R2.B06_311_01_XRCC6.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346259"
gz1="$(_compress_if_exists 'SRR3346259_1' || true)"
gz2="$(_compress_if_exists 'SRR3346259_2' || true)"
gzs="$(_compress_if_exists 'SRR3346259' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "311_CLIP_ATTCAGAA-ATAGAGGC_L001_R1.C01_311_02_XRCC6.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "311_CLIP_ATTCAGAA-ATAGAGGC_L001_R2.C01_311_02_XRCC6.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346260"
gz1="$(_compress_if_exists 'SRR3346260_1' || true)"
gz2="$(_compress_if_exists 'SRR3346260_2' || true)"
gzs="$(_compress_if_exists 'SRR3346260' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "311_CLIP_ATTCAGAA-ATAGAGGC_L001_R1.D08fixed_311_02_XRCC6.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "311_CLIP_ATTCAGAA-ATAGAGGC_L001_R2.D08fixed_311_02_XRCC6.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346261"
gz1="$(_compress_if_exists 'SRR3346261_1' || true)"
gz2="$(_compress_if_exists 'SRR3346261_2' || true)"
gzs="$(_compress_if_exists 'SRR3346261' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "311_INPUT_GAATTCGT-ATAGAGGC_L001_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "311_INPUT_GAATTCGT-ATAGAGGC_L001_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346262"
gz1="$(_compress_if_exists 'SRR3346262_1' || true)"
gz2="$(_compress_if_exists 'SRR3346262_2' || true)"
gzs="$(_compress_if_exists 'SRR3346262' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "383_CLIP_TCCGGAGA-TAATCTTA_L006_R1.A04_383_01_DGCR8.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "383_CLIP_TCCGGAGA-TAATCTTA_L006_R2.A04_383_01_DGCR8.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346263"
gz1="$(_compress_if_exists 'SRR3346263_1' || true)"
gz2="$(_compress_if_exists 'SRR3346263_2' || true)"
gzs="$(_compress_if_exists 'SRR3346263' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "383_CLIP_TCCGGAGA-TAATCTTA_L006_R1.F05_383_01_DGCR8.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "383_CLIP_TCCGGAGA-TAATCTTA_L006_R2.F05_383_01_DGCR8.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346264"
gz1="$(_compress_if_exists 'SRR3346264_1' || true)"
gz2="$(_compress_if_exists 'SRR3346264_2' || true)"
gzs="$(_compress_if_exists 'SRR3346264' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "383_CLIP_TCCGGAGA-TAATCTTA_L006_R1.A03_383_02_DGCR8.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "383_CLIP_TCCGGAGA-TAATCTTA_L006_R2.A03_383_02_DGCR8.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346265"
gz1="$(_compress_if_exists 'SRR3346265_1' || true)"
gz2="$(_compress_if_exists 'SRR3346265_2' || true)"
gzs="$(_compress_if_exists 'SRR3346265' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "383_CLIP_TCCGGAGA-TAATCTTA_L006_R1.G07_383_02_DGCR8.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "383_CLIP_TCCGGAGA-TAATCTTA_L006_R2.G07_383_02_DGCR8.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346266"
gz1="$(_compress_if_exists 'SRR3346266_1' || true)"
gz2="$(_compress_if_exists 'SRR3346266_2' || true)"
gzs="$(_compress_if_exists 'SRR3346266' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "383_INPUT_TCCGGAGA-AGGCGAAG_L006_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "383_INPUT_TCCGGAGA-AGGCGAAG_L006_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346267"
gz1="$(_compress_if_exists 'SRR3346267_1' || true)"
gz2="$(_compress_if_exists 'SRR3346267_2' || true)"
gzs="$(_compress_if_exists 'SRR3346267' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "415_CLIP_GAATTCGT-ATAGAGGC_L006_R1.A03_415_01_TNRC6A.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "415_CLIP_GAATTCGT-ATAGAGGC_L006_R2.A03_415_01_TNRC6A.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346268"
gz1="$(_compress_if_exists 'SRR3346268_1' || true)"
gz2="$(_compress_if_exists 'SRR3346268_2' || true)"
gzs="$(_compress_if_exists 'SRR3346268' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "415_CLIP_GAATTCGT-ATAGAGGC_L006_R1.G07_415_01_TNRC6A.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "415_CLIP_GAATTCGT-ATAGAGGC_L006_R2.G07_415_01_TNRC6A.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346269"
gz1="$(_compress_if_exists 'SRR3346269_1' || true)"
gz2="$(_compress_if_exists 'SRR3346269_2' || true)"
gzs="$(_compress_if_exists 'SRR3346269' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "415_CLIP_GAATTCGT-ATAGAGGC_L006_R1.A04_415_02_TNRC6A.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "415_CLIP_GAATTCGT-ATAGAGGC_L006_R2.A04_415_02_TNRC6A.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346270"
gz1="$(_compress_if_exists 'SRR3346270_1' || true)"
gz2="$(_compress_if_exists 'SRR3346270_2' || true)"
gzs="$(_compress_if_exists 'SRR3346270' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "415_CLIP_GAATTCGT-ATAGAGGC_L006_R1.F05_415_02_TNRC6A.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "415_CLIP_GAATTCGT-ATAGAGGC_L006_R2.F05_415_02_TNRC6A.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346271"
gz1="$(_compress_if_exists 'SRR3346271_1' || true)"
gz2="$(_compress_if_exists 'SRR3346271_2' || true)"
gzs="$(_compress_if_exists 'SRR3346271' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "415_INPUT_ATTCAGAA-ATAGAGGC_L006_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "415_INPUT_ATTCAGAA-ATAGAGGC_L006_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346272"
gz1="$(_compress_if_exists 'SRR3346272_1' || true)"
gz2="$(_compress_if_exists 'SRR3346272_2' || true)"
gzs="$(_compress_if_exists 'SRR3346272' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "417_CLIP_S55_L006_R1_001.A01_417_01_POLR2G.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "417_CLIP_S55_L006_R2_001.A01_417_01_POLR2G.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346273"
gz1="$(_compress_if_exists 'SRR3346273_1' || true)"
gz2="$(_compress_if_exists 'SRR3346273_2' || true)"
gzs="$(_compress_if_exists 'SRR3346273' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "417_CLIP_S55_L006_R1_001.B06_417_01_POLR2G.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "417_CLIP_S55_L006_R2_001.B06_417_01_POLR2G.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346274"
gz1="$(_compress_if_exists 'SRR3346274_1' || true)"
gz2="$(_compress_if_exists 'SRR3346274_2' || true)"
gzs="$(_compress_if_exists 'SRR3346274' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "417_CLIP_S55_L006_R1_001.C01_417_02_POLR2G.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "417_CLIP_S55_L006_R2_001.C01_417_02_POLR2G.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346275"
gz1="$(_compress_if_exists 'SRR3346275_1' || true)"
gz2="$(_compress_if_exists 'SRR3346275_2' || true)"
gzs="$(_compress_if_exists 'SRR3346275' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "417_CLIP_S55_L006_R1_001.D08fixed_417_02_POLR2G.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "417_CLIP_S55_L006_R2_001.D08fixed_417_02_POLR2G.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346276"
gz1="$(_compress_if_exists 'SRR3346276_1' || true)"
gz2="$(_compress_if_exists 'SRR3346276_2' || true)"
gzs="$(_compress_if_exists 'SRR3346276' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "417_INPUT_S56_L006_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "417_INPUT_S56_L006_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346277"
gz1="$(_compress_if_exists 'SRR3346277_1' || true)"
gz2="$(_compress_if_exists 'SRR3346277_2' || true)"
gzs="$(_compress_if_exists 'SRR3346277' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "440_CLIP_TCCGGAGA-AGGCGAAG_L003_R1.A01_440_01_EWSR1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "440_CLIP_TCCGGAGA-AGGCGAAG_L003_R2.A01_440_01_EWSR1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346278"
gz1="$(_compress_if_exists 'SRR3346278_1' || true)"
gz2="$(_compress_if_exists 'SRR3346278_2' || true)"
gzs="$(_compress_if_exists 'SRR3346278' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "440_CLIP_TCCGGAGA-AGGCGAAG_L003_R1.B06_440_01_EWSR1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "440_CLIP_TCCGGAGA-AGGCGAAG_L003_R2.B06_440_01_EWSR1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346279"
gz1="$(_compress_if_exists 'SRR3346279_1' || true)"
gz2="$(_compress_if_exists 'SRR3346279_2' || true)"
gzs="$(_compress_if_exists 'SRR3346279' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "440_CLIP_TCCGGAGA-AGGCGAAG_L003_R1.C01_440_02_EWSR1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "440_CLIP_TCCGGAGA-AGGCGAAG_L003_R2.C01_440_02_EWSR1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346280"
gz1="$(_compress_if_exists 'SRR3346280_1' || true)"
gz2="$(_compress_if_exists 'SRR3346280_2' || true)"
gzs="$(_compress_if_exists 'SRR3346280' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "440_CLIP_TCCGGAGA-AGGCGAAG_L003_R1.D08fixed_440_02_EWSR1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "440_CLIP_TCCGGAGA-AGGCGAAG_L003_R2.D08fixed_440_02_EWSR1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346281"
gz1="$(_compress_if_exists 'SRR3346281_1' || true)"
gz2="$(_compress_if_exists 'SRR3346281_2' || true)"
gzs="$(_compress_if_exists 'SRR3346281' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "440_INPUT_ATTACTCG-TAATCTTA_L005_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "440_INPUT_ATTACTCG-TAATCTTA_L005_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346282"
gz1="$(_compress_if_exists 'SRR3346282_1' || true)"
gz2="$(_compress_if_exists 'SRR3346282_2' || true)"
gzs="$(_compress_if_exists 'SRR3346282' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "441_CLIP_CGCTCATT-TATAGCCT_L007_R1.A03_441_01_PUM2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "441_CLIP_CGCTCATT-TATAGCCT_L007_R2.A03_441_01_PUM2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346283"
gz1="$(_compress_if_exists 'SRR3346283_1' || true)"
gz2="$(_compress_if_exists 'SRR3346283_2' || true)"
gzs="$(_compress_if_exists 'SRR3346283' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "441_CLIP_CGCTCATT-TATAGCCT_L007_R1.G07_441_01_PUM2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "441_CLIP_CGCTCATT-TATAGCCT_L007_R2.G07_441_01_PUM2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346284"
gz1="$(_compress_if_exists 'SRR3346284_1' || true)"
gz2="$(_compress_if_exists 'SRR3346284_2' || true)"
gzs="$(_compress_if_exists 'SRR3346284' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "441_CLIP_CGCTCATT-TATAGCCT_L007_R1.A04_441_02_PUM2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "441_CLIP_CGCTCATT-TATAGCCT_L007_R2.A04_441_02_PUM2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346285"
gz1="$(_compress_if_exists 'SRR3346285_1' || true)"
gz2="$(_compress_if_exists 'SRR3346285_2' || true)"
gzs="$(_compress_if_exists 'SRR3346285' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "441_CLIP_CGCTCATT-TATAGCCT_L007_R1.F05_441_02_PUM2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "441_CLIP_CGCTCATT-TATAGCCT_L007_R2.F05_441_02_PUM2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346286"
gz1="$(_compress_if_exists 'SRR3346286_1' || true)"
gz2="$(_compress_if_exists 'SRR3346286_2' || true)"
gzs="$(_compress_if_exists 'SRR3346286' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "441_INPUT_GAGATTCC-ATAGAGGC_L007_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "441_INPUT_GAGATTCC-ATAGAGGC_L007_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346287"
gz1="$(_compress_if_exists 'SRR3346287_1' || true)"
gz2="$(_compress_if_exists 'SRR3346287_2' || true)"
gzs="$(_compress_if_exists 'SRR3346287' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "450_CLIP_GAGATTCC-ATAGAGGC_L004_R1.A01_450_01_GPKOW.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "450_CLIP_GAGATTCC-ATAGAGGC_L004_R2.A01_450_01_GPKOW.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346288"
gz1="$(_compress_if_exists 'SRR3346288_1' || true)"
gz2="$(_compress_if_exists 'SRR3346288_2' || true)"
gzs="$(_compress_if_exists 'SRR3346288' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "450_CLIP_GAGATTCC-ATAGAGGC_L004_R1.B06_450_01_GPKOW.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "450_CLIP_GAGATTCC-ATAGAGGC_L004_R2.B06_450_01_GPKOW.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346289"
gz1="$(_compress_if_exists 'SRR3346289_1' || true)"
gz2="$(_compress_if_exists 'SRR3346289_2' || true)"
gzs="$(_compress_if_exists 'SRR3346289' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "450_CLIP_GAGATTCC-ATAGAGGC_L004_R1.C01_450_02_GPKOW.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "450_CLIP_GAGATTCC-ATAGAGGC_L004_R2.C01_450_02_GPKOW.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346290"
gz1="$(_compress_if_exists 'SRR3346290_1' || true)"
gz2="$(_compress_if_exists 'SRR3346290_2' || true)"
gzs="$(_compress_if_exists 'SRR3346290' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "450_CLIP_GAGATTCC-ATAGAGGC_L004_R1.D08fixed_450_02_GPKOW.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "450_CLIP_GAGATTCC-ATAGAGGC_L004_R2.D08fixed_450_02_GPKOW.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346291"
gz1="$(_compress_if_exists 'SRR3346291_1' || true)"
gz2="$(_compress_if_exists 'SRR3346291_2' || true)"
gzs="$(_compress_if_exists 'SRR3346291' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "450_INPUT_CGCTCATT-TATAGCCT_L004_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "450_INPUT_CGCTCATT-TATAGCCT_L004_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346292"
gz1="$(_compress_if_exists 'SRR3346292_1' || true)"
gz2="$(_compress_if_exists 'SRR3346292_2' || true)"
gzs="$(_compress_if_exists 'SRR3346292' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "452_CLIP_GAGATTCC-GGCTCTGA_L005_R1.A01_452_01_NSUN2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "452_CLIP_GAGATTCC-GGCTCTGA_L005_R2.A01_452_01_NSUN2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346293"
gz1="$(_compress_if_exists 'SRR3346293_1' || true)"
gz2="$(_compress_if_exists 'SRR3346293_2' || true)"
gzs="$(_compress_if_exists 'SRR3346293' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "452_CLIP_GAGATTCC-GGCTCTGA_L005_R1.B06_452_01_NSUN2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "452_CLIP_GAGATTCC-GGCTCTGA_L005_R2.B06_452_01_NSUN2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346294"
gz1="$(_compress_if_exists 'SRR3346294_1' || true)"
gz2="$(_compress_if_exists 'SRR3346294_2' || true)"
gzs="$(_compress_if_exists 'SRR3346294' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "452_CLIP_GAGATTCC-GGCTCTGA_L005_R1.C01_452_02_NSUN2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "452_CLIP_GAGATTCC-GGCTCTGA_L005_R2.C01_452_02_NSUN2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346295"
gz1="$(_compress_if_exists 'SRR3346295_1' || true)"
gz2="$(_compress_if_exists 'SRR3346295_2' || true)"
gzs="$(_compress_if_exists 'SRR3346295' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "452_CLIP_GAGATTCC-GGCTCTGA_L005_R1.D08fixed_452_02_NSUN2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "452_CLIP_GAGATTCC-GGCTCTGA_L005_R2.D08fixed_452_02_NSUN2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346296"
gz1="$(_compress_if_exists 'SRR3346296_1' || true)"
gz2="$(_compress_if_exists 'SRR3346296_2' || true)"
gzs="$(_compress_if_exists 'SRR3346296' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "452_INPUT_CGCTCATT-CCTATCCT_L005_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "452_INPUT_CGCTCATT-CCTATCCT_L005_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346297"
gz1="$(_compress_if_exists 'SRR3346297_1' || true)"
gz2="$(_compress_if_exists 'SRR3346297_2' || true)"
gzs="$(_compress_if_exists 'SRR3346297' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "464_CLIP_GAGATTCC-TAATCTTA_L002_R1.C01_464_01_FTO.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "464_CLIP_GAGATTCC-TAATCTTA_L002_R2.C01_464_01_FTO.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346298"
gz1="$(_compress_if_exists 'SRR3346298_1' || true)"
gz2="$(_compress_if_exists 'SRR3346298_2' || true)"
gzs="$(_compress_if_exists 'SRR3346298' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "464_CLIP_GAGATTCC-TAATCTTA_L002_R1.D08fixed_464_01_FTO.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "464_CLIP_GAGATTCC-TAATCTTA_L002_R2.D08fixed_464_01_FTO.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346299"
gz1="$(_compress_if_exists 'SRR3346299_1' || true)"
gz2="$(_compress_if_exists 'SRR3346299_2' || true)"
gzs="$(_compress_if_exists 'SRR3346299' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "464_CLIP_GAGATTCC-TAATCTTA_L002_R1.A01_464_02_FTO.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "464_CLIP_GAGATTCC-TAATCTTA_L002_R2.A01_464_02_FTO.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346300"
gz1="$(_compress_if_exists 'SRR3346300_1' || true)"
gz2="$(_compress_if_exists 'SRR3346300_2' || true)"
gzs="$(_compress_if_exists 'SRR3346300' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "464_CLIP_GAGATTCC-TAATCTTA_L002_R1.B06_464_02_FTO.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "464_CLIP_GAGATTCC-TAATCTTA_L002_R2.B06_464_02_FTO.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346301"
gz1="$(_compress_if_exists 'SRR3346301_1' || true)"
gz2="$(_compress_if_exists 'SRR3346301_2' || true)"
gzs="$(_compress_if_exists 'SRR3346301' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "464_INPUT_CGCTCATT-AGGCGAAG_L002_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "464_INPUT_CGCTCATT-AGGCGAAG_L002_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346302"
gz1="$(_compress_if_exists 'SRR3346302_1' || true)"
gz2="$(_compress_if_exists 'SRR3346302_2' || true)"
gzs="$(_compress_if_exists 'SRR3346302' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "465_CLIP_CGCTCATT-TAATCTTA_L001_R1.A03_465_01_UPF1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "465_CLIP_CGCTCATT-TAATCTTA_L001_R2.A03_465_01_UPF1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346303"
gz1="$(_compress_if_exists 'SRR3346303_1' || true)"
gz2="$(_compress_if_exists 'SRR3346303_2' || true)"
gzs="$(_compress_if_exists 'SRR3346303' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "465_CLIP_CGCTCATT-TAATCTTA_L001_R1.G07_465_01_UPF1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "465_CLIP_CGCTCATT-TAATCTTA_L001_R2.G07_465_01_UPF1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346304"
gz1="$(_compress_if_exists 'SRR3346304_1' || true)"
gz2="$(_compress_if_exists 'SRR3346304_2' || true)"
gzs="$(_compress_if_exists 'SRR3346304' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "465_CLIP_CGCTCATT-TAATCTTA_L001_R1.A04_465_02_UPF1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "465_CLIP_CGCTCATT-TAATCTTA_L001_R2.A04_465_02_UPF1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346305"
gz1="$(_compress_if_exists 'SRR3346305_1' || true)"
gz2="$(_compress_if_exists 'SRR3346305_2' || true)"
gzs="$(_compress_if_exists 'SRR3346305' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "465_CLIP_CGCTCATT-TAATCTTA_L001_R1.F05_465_02_UPF1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "465_CLIP_CGCTCATT-TAATCTTA_L001_R2.F05_465_02_UPF1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346306"
gz1="$(_compress_if_exists 'SRR3346306_1' || true)"
gz2="$(_compress_if_exists 'SRR3346306_2' || true)"
gzs="$(_compress_if_exists 'SRR3346306' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "465_INPUT_GAGATTCC-AGGCGAAG_L001_R1.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "465_INPUT_GAGATTCC-AGGCGAAG_L001_R2.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346307"
gz1="$(_compress_if_exists 'SRR3346307_1' || true)"
gz2="$(_compress_if_exists 'SRR3346307_2' || true)"
gzs="$(_compress_if_exists 'SRR3346307' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "466_CLIP_S25_L003_R1_001.A01_466_01_QKI.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "466_CLIP_S25_L003_R2_001.A01_466_01_QKI.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346308"
gz1="$(_compress_if_exists 'SRR3346308_1' || true)"
gz2="$(_compress_if_exists 'SRR3346308_2' || true)"
gzs="$(_compress_if_exists 'SRR3346308' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "466_CLIP_S25_L003_R1_001.B06_466_01_QKI.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "466_CLIP_S25_L003_R2_001.B06_466_01_QKI.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346309"
gz1="$(_compress_if_exists 'SRR3346309_1' || true)"
gz2="$(_compress_if_exists 'SRR3346309_2' || true)"
gzs="$(_compress_if_exists 'SRR3346309' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "466_CLIP_S25_L003_R1_001.C01_466_02_QKI.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "466_CLIP_S25_L003_R2_001.C01_466_02_QKI.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346310"
gz1="$(_compress_if_exists 'SRR3346310_1' || true)"
gz2="$(_compress_if_exists 'SRR3346310_2' || true)"
gzs="$(_compress_if_exists 'SRR3346310' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "466_CLIP_S25_L003_R1_001.D08fixed_466_02_QKI.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "466_CLIP_S25_L003_R2_001.D08fixed_466_02_QKI.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346311"
gz1="$(_compress_if_exists 'SRR3346311_1' || true)"
gz2="$(_compress_if_exists 'SRR3346311_2' || true)"
gzs="$(_compress_if_exists 'SRR3346311' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "466_INPUT_S26_L003_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "466_INPUT_S26_L003_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346312"
gz1="$(_compress_if_exists 'SRR3346312_1' || true)"
gz2="$(_compress_if_exists 'SRR3346312_2' || true)"
gzs="$(_compress_if_exists 'SRR3346312' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "477_CLIP_S49_L006_R1_001.A03_477_01_NCBP2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "477_CLIP_S49_L006_R2_001.A03_477_01_NCBP2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346313"
gz1="$(_compress_if_exists 'SRR3346313_1' || true)"
gz2="$(_compress_if_exists 'SRR3346313_2' || true)"
gzs="$(_compress_if_exists 'SRR3346313' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "477_CLIP_S49_L006_R1_001.G07_477_01_NCBP2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "477_CLIP_S49_L006_R2_001.G07_477_01_NCBP2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346314"
gz1="$(_compress_if_exists 'SRR3346314_1' || true)"
gz2="$(_compress_if_exists 'SRR3346314_2' || true)"
gzs="$(_compress_if_exists 'SRR3346314' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "477_CLIP_S49_L006_R1_001.A04_477_02_NCBP2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "477_CLIP_S49_L006_R2_001.A04_477_02_NCBP2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346315"
gz1="$(_compress_if_exists 'SRR3346315_1' || true)"
gz2="$(_compress_if_exists 'SRR3346315_2' || true)"
gzs="$(_compress_if_exists 'SRR3346315' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "477_CLIP_S49_L006_R1_001.F05_477_02_NCBP2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "477_CLIP_S49_L006_R2_001.F05_477_02_NCBP2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346316"
gz1="$(_compress_if_exists 'SRR3346316_1' || true)"
gz2="$(_compress_if_exists 'SRR3346316_2' || true)"
gzs="$(_compress_if_exists 'SRR3346316' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "477_INPUT_S50_L006_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "477_INPUT_S50_L006_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346317"
gz1="$(_compress_if_exists 'SRR3346317_1' || true)"
gz2="$(_compress_if_exists 'SRR3346317_2' || true)"
gzs="$(_compress_if_exists 'SRR3346317' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "478_CLIP_S51_L006_R1_001.A04_478_01_QKI.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "478_CLIP_S51_L006_R2_001.A04_478_01_QKI.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346318"
gz1="$(_compress_if_exists 'SRR3346318_1' || true)"
gz2="$(_compress_if_exists 'SRR3346318_2' || true)"
gzs="$(_compress_if_exists 'SRR3346318' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "478_CLIP_S51_L006_R1_001.F05_478_01_QKI.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "478_CLIP_S51_L006_R2_001.F05_478_01_QKI.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346319"
gz1="$(_compress_if_exists 'SRR3346319_1' || true)"
gz2="$(_compress_if_exists 'SRR3346319_2' || true)"
gzs="$(_compress_if_exists 'SRR3346319' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "478_CLIP_S51_L006_R1_001.A03_478_02_QKI.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "478_CLIP_S51_L006_R2_001.A03_478_02_QKI.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346320"
gz1="$(_compress_if_exists 'SRR3346320_1' || true)"
gz2="$(_compress_if_exists 'SRR3346320_2' || true)"
gzs="$(_compress_if_exists 'SRR3346320' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "478_CLIP_S51_L006_R1_001.G07_478_02_QKI.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "478_CLIP_S51_L006_R2_001.G07_478_02_QKI.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346321"
gz1="$(_compress_if_exists 'SRR3346321_1' || true)"
gz2="$(_compress_if_exists 'SRR3346321_2' || true)"
gzs="$(_compress_if_exists 'SRR3346321' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "478_INPUT_S52_L006_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "478_INPUT_S52_L006_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346322"
gz1="$(_compress_if_exists 'SRR3346322_1' || true)"
gz2="$(_compress_if_exists 'SRR3346322_2' || true)"
gzs="$(_compress_if_exists 'SRR3346322' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "480_CLIP_S60_L007_R1_001.A01_480_01_XRCC6.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "480_CLIP_S60_L007_R2_001.A01_480_01_XRCC6.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346323"
gz1="$(_compress_if_exists 'SRR3346323_1' || true)"
gz2="$(_compress_if_exists 'SRR3346323_2' || true)"
gzs="$(_compress_if_exists 'SRR3346323' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "480_CLIP_S60_L007_R1_001.B06_480_01_XRCC6.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "480_CLIP_S60_L007_R2_001.B06_480_01_XRCC6.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346324"
gz1="$(_compress_if_exists 'SRR3346324_1' || true)"
gz2="$(_compress_if_exists 'SRR3346324_2' || true)"
gzs="$(_compress_if_exists 'SRR3346324' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "480_CLIP_S60_L007_R1_001.C01_480_02_XRCC6.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "480_CLIP_S60_L007_R2_001.C01_480_02_XRCC6.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346325"
gz1="$(_compress_if_exists 'SRR3346325_1' || true)"
gz2="$(_compress_if_exists 'SRR3346325_2' || true)"
gzs="$(_compress_if_exists 'SRR3346325' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "480_CLIP_S60_L007_R1_001.D08fixed_480_02_XRCC6.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "480_CLIP_S60_L007_R2_001.D08fixed_480_02_XRCC6.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346326"
gz1="$(_compress_if_exists 'SRR3346326_1' || true)"
gz2="$(_compress_if_exists 'SRR3346326_2' || true)"
gzs="$(_compress_if_exists 'SRR3346326' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "480_INPUT_S61_L007_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "480_INPUT_S61_L007_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346327"
gz1="$(_compress_if_exists 'SRR3346327_1' || true)"
gz2="$(_compress_if_exists 'SRR3346327_2' || true)"
gzs="$(_compress_if_exists 'SRR3346327' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "481_CLIP_S62_L007_R1_001.A01_481_01_DROSHA.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "481_CLIP_S62_L007_R2_001.A01_481_01_DROSHA.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346328"
gz1="$(_compress_if_exists 'SRR3346328_1' || true)"
gz2="$(_compress_if_exists 'SRR3346328_2' || true)"
gzs="$(_compress_if_exists 'SRR3346328' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "481_CLIP_S62_L007_R1_001.B06_481_01_DROSHA.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "481_CLIP_S62_L007_R2_001.B06_481_01_DROSHA.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346329"
gz1="$(_compress_if_exists 'SRR3346329_1' || true)"
gz2="$(_compress_if_exists 'SRR3346329_2' || true)"
gzs="$(_compress_if_exists 'SRR3346329' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "481_CLIP_S62_L007_R1_001.C01_481_02_DROSHA.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "481_CLIP_S62_L007_R2_001.C01_481_02_DROSHA.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346330"
gz1="$(_compress_if_exists 'SRR3346330_1' || true)"
gz2="$(_compress_if_exists 'SRR3346330_2' || true)"
gzs="$(_compress_if_exists 'SRR3346330' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "481_CLIP_S62_L007_R1_001.D08fixed_481_02_DROSHA.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "481_CLIP_S62_L007_R2_001.D08fixed_481_02_DROSHA.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346331"
gz1="$(_compress_if_exists 'SRR3346331_1' || true)"
gz2="$(_compress_if_exists 'SRR3346331_2' || true)"
gzs="$(_compress_if_exists 'SRR3346331' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "481_INPUT_S63_L007_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "481_INPUT_S63_L007_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346332"
gz1="$(_compress_if_exists 'SRR3346332_1' || true)"
gz2="$(_compress_if_exists 'SRR3346332_2' || true)"
gzs="$(_compress_if_exists 'SRR3346332' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "484_CLIP_S6_L001_R1_001.A01_484_01_POLR2G.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "484_CLIP_S6_L001_R2_001.A01_484_01_POLR2G.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346333"
gz1="$(_compress_if_exists 'SRR3346333_1' || true)"
gz2="$(_compress_if_exists 'SRR3346333_2' || true)"
gzs="$(_compress_if_exists 'SRR3346333' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "484_CLIP_S6_L001_R1_001.B06_484_01_POLR2G.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "484_CLIP_S6_L001_R2_001.B06_484_01_POLR2G.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346334"
gz1="$(_compress_if_exists 'SRR3346334_1' || true)"
gz2="$(_compress_if_exists 'SRR3346334_2' || true)"
gzs="$(_compress_if_exists 'SRR3346334' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "484_CLIP_S6_L001_R1_001.C01_484_02_POLR2G.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "484_CLIP_S6_L001_R2_001.C01_484_02_POLR2G.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346335"
gz1="$(_compress_if_exists 'SRR3346335_1' || true)"
gz2="$(_compress_if_exists 'SRR3346335_2' || true)"
gzs="$(_compress_if_exists 'SRR3346335' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "484_CLIP_S6_L001_R1_001.D08fixed_484_02_POLR2G.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "484_CLIP_S6_L001_R2_001.D08fixed_484_02_POLR2G.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346336"
gz1="$(_compress_if_exists 'SRR3346336_1' || true)"
gz2="$(_compress_if_exists 'SRR3346336_2' || true)"
gzs="$(_compress_if_exists 'SRR3346336' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "484_INPUT_S7_L001_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "484_INPUT_S7_L001_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346337"
gz1="$(_compress_if_exists 'SRR3346337_1' || true)"
gz2="$(_compress_if_exists 'SRR3346337_2' || true)"
gzs="$(_compress_if_exists 'SRR3346337' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "492_CLIP_S11_L002_R1_001.A04_492_01_DDX3X.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "492_CLIP_S11_L002_R2_001.A04_492_01_DDX3X.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346338"
gz1="$(_compress_if_exists 'SRR3346338_1' || true)"
gz2="$(_compress_if_exists 'SRR3346338_2' || true)"
gzs="$(_compress_if_exists 'SRR3346338' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "492_CLIP_S11_L002_R1_001.F05_492_01_DDX3X.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "492_CLIP_S11_L002_R2_001.F05_492_01_DDX3X.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346339"
gz1="$(_compress_if_exists 'SRR3346339_1' || true)"
gz2="$(_compress_if_exists 'SRR3346339_2' || true)"
gzs="$(_compress_if_exists 'SRR3346339' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "492_CLIP_S11_L002_R1_001.A03_492_02_DDX3X.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "492_CLIP_S11_L002_R2_001.A03_492_02_DDX3X.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346340"
gz1="$(_compress_if_exists 'SRR3346340_1' || true)"
gz2="$(_compress_if_exists 'SRR3346340_2' || true)"
gzs="$(_compress_if_exists 'SRR3346340' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "492_CLIP_S11_L002_R1_001.G07_492_02_DDX3X.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "492_CLIP_S11_L002_R2_001.G07_492_02_DDX3X.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346341"
gz1="$(_compress_if_exists 'SRR3346341_1' || true)"
gz2="$(_compress_if_exists 'SRR3346341_2' || true)"
gzs="$(_compress_if_exists 'SRR3346341' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "492_INPUT_S12_L002_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "492_INPUT_S12_L002_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346342"
gz1="$(_compress_if_exists 'SRR3346342_1' || true)"
gz2="$(_compress_if_exists 'SRR3346342_2' || true)"
gzs="$(_compress_if_exists 'SRR3346342' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "494_CLIP_S19_L003_R1_001.A03_494_01_RBM22.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "494_CLIP_S19_L003_R2_001.A03_494_01_RBM22.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346343"
gz1="$(_compress_if_exists 'SRR3346343_1' || true)"
gz2="$(_compress_if_exists 'SRR3346343_2' || true)"
gzs="$(_compress_if_exists 'SRR3346343' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "494_CLIP_S19_L003_R1_001.G07_494_01_RBM22.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "494_CLIP_S19_L003_R2_001.G07_494_01_RBM22.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346344"
gz1="$(_compress_if_exists 'SRR3346344_1' || true)"
gz2="$(_compress_if_exists 'SRR3346344_2' || true)"
gzs="$(_compress_if_exists 'SRR3346344' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "494_CLIP_S19_L003_R1_001.A04_494_02_RBM22.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "494_CLIP_S19_L003_R2_001.A04_494_02_RBM22.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346345"
gz1="$(_compress_if_exists 'SRR3346345_1' || true)"
gz2="$(_compress_if_exists 'SRR3346345_2' || true)"
gzs="$(_compress_if_exists 'SRR3346345' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "494_CLIP_S19_L003_R1_001.F05_494_02_RBM22.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "494_CLIP_S19_L003_R2_001.F05_494_02_RBM22.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346346"
gz1="$(_compress_if_exists 'SRR3346346_1' || true)"
gz2="$(_compress_if_exists 'SRR3346346_2' || true)"
gzs="$(_compress_if_exists 'SRR3346346' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "494_INPUT_S20_L003_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "494_INPUT_S20_L003_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346347"
gz1="$(_compress_if_exists 'SRR3346347_1' || true)"
gz2="$(_compress_if_exists 'SRR3346347_2' || true)"
gzs="$(_compress_if_exists 'SRR3346347' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "495_CLIP_S21_L003_R1_001.A04_495_01_PPIG.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "495_CLIP_S21_L003_R2_001.A04_495_01_PPIG.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346348"
gz1="$(_compress_if_exists 'SRR3346348_1' || true)"
gz2="$(_compress_if_exists 'SRR3346348_2' || true)"
gzs="$(_compress_if_exists 'SRR3346348' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "495_CLIP_S21_L003_R1_001.F05_495_01_PPIG.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "495_CLIP_S21_L003_R2_001.F05_495_01_PPIG.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346349"
gz1="$(_compress_if_exists 'SRR3346349_1' || true)"
gz2="$(_compress_if_exists 'SRR3346349_2' || true)"
gzs="$(_compress_if_exists 'SRR3346349' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "495_CLIP_S21_L003_R1_001.A03_495_02_PPIG.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "495_CLIP_S21_L003_R2_001.A03_495_02_PPIG.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346350"
gz1="$(_compress_if_exists 'SRR3346350_1' || true)"
gz2="$(_compress_if_exists 'SRR3346350_2' || true)"
gzs="$(_compress_if_exists 'SRR3346350' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "495_CLIP_S21_L003_R1_001.G07_495_02_PPIG.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "495_CLIP_S21_L003_R2_001.G07_495_02_PPIG.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346351"
gz1="$(_compress_if_exists 'SRR3346351_1' || true)"
gz2="$(_compress_if_exists 'SRR3346351_2' || true)"
gzs="$(_compress_if_exists 'SRR3346351' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "495_INPUT_S22_L003_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "495_INPUT_S22_L003_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346352"
gz1="$(_compress_if_exists 'SRR3346352_1' || true)"
gz2="$(_compress_if_exists 'SRR3346352_2' || true)"
gzs="$(_compress_if_exists 'SRR3346352' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "506_CLIP_S64_L007_R1_001.A03_506_01_SF3B1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "506_CLIP_S64_L007_R2_001.A03_506_01_SF3B1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346353"
gz1="$(_compress_if_exists 'SRR3346353_1' || true)"
gz2="$(_compress_if_exists 'SRR3346353_2' || true)"
gzs="$(_compress_if_exists 'SRR3346353' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "506_CLIP_S64_L007_R1_001.G07_506_01_SF3B1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "506_CLIP_S64_L007_R2_001.G07_506_01_SF3B1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346354"
gz1="$(_compress_if_exists 'SRR3346354_1' || true)"
gz2="$(_compress_if_exists 'SRR3346354_2' || true)"
gzs="$(_compress_if_exists 'SRR3346354' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "506_CLIP_S64_L007_R1_001.A04_506_02_SF3B1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "506_CLIP_S64_L007_R2_001.A04_506_02_SF3B1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346355"
gz1="$(_compress_if_exists 'SRR3346355_1' || true)"
gz2="$(_compress_if_exists 'SRR3346355_2' || true)"
gzs="$(_compress_if_exists 'SRR3346355' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "506_CLIP_S64_L007_R1_001.F05_506_02_SF3B1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "506_CLIP_S64_L007_R2_001.F05_506_02_SF3B1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346356"
gz1="$(_compress_if_exists 'SRR3346356_1' || true)"
gz2="$(_compress_if_exists 'SRR3346356_2' || true)"
gzs="$(_compress_if_exists 'SRR3346356' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "506_INPUT_S65_L007_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "506_INPUT_S65_L007_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346357"
gz1="$(_compress_if_exists 'SRR3346357_1' || true)"
gz2="$(_compress_if_exists 'SRR3346357_2' || true)"
gzs="$(_compress_if_exists 'SRR3346357' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "508_CLIP_S31_L004_R1_001.A01_508_01_BUD13.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "508_CLIP_S31_L004_R2_001.A01_508_01_BUD13.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346358"
gz1="$(_compress_if_exists 'SRR3346358_1' || true)"
gz2="$(_compress_if_exists 'SRR3346358_2' || true)"
gzs="$(_compress_if_exists 'SRR3346358' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "508_CLIP_S31_L004_R1_001.B06_508_01_BUD13.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "508_CLIP_S31_L004_R2_001.B06_508_01_BUD13.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346359"
gz1="$(_compress_if_exists 'SRR3346359_1' || true)"
gz2="$(_compress_if_exists 'SRR3346359_2' || true)"
gzs="$(_compress_if_exists 'SRR3346359' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "508_CLIP_S31_L004_R1_001.C01_508_02_BUD13.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "508_CLIP_S31_L004_R2_001.C01_508_02_BUD13.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346360"
gz1="$(_compress_if_exists 'SRR3346360_1' || true)"
gz2="$(_compress_if_exists 'SRR3346360_2' || true)"
gzs="$(_compress_if_exists 'SRR3346360' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "508_CLIP_S31_L004_R1_001.D08fixed_508_02_BUD13.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "508_CLIP_S31_L004_R2_001.D08fixed_508_02_BUD13.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR3346361"
gz1="$(_compress_if_exists 'SRR3346361_1' || true)"
gz2="$(_compress_if_exists 'SRR3346361_2' || true)"
gzs="$(_compress_if_exists 'SRR3346361' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "508_INPUT_S32_L004_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "508_INPUT_S32_L004_R2_001.unassigned.randomer.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346257/SRR3346257"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346258/SRR3346258"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346259/SRR3346259"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346260/SRR3346260"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346261/SRR3346261"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346262/SRR3346262"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346263/SRR3346263"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346264/SRR3346264"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346265/SRR3346265"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346266/SRR3346266"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346267/SRR3346267"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346268/SRR3346268"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346269/SRR3346269"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346270/SRR3346270"
curl -L -O -C - "https://sra-pub-src-1.s3.amazonaws.com/SRR3346271/415_INPUT_ATTCAGAA-ATAGAGGC_L006_R1.unassigned.randomer.fastq.gz.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346272/SRR3346272"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346273/SRR3346273"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346274/SRR3346274"
curl -L -O -C - "https://sra-pub-src-1.s3.amazonaws.com/SRR3346275/417_CLIP_S55_L006_R1_001.D08fixed_417_02_POLR2G.randomer.fastq.gz.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346276/SRR3346276"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346277/SRR3346277"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346278/SRR3346278"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346279/SRR3346279"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346280/SRR3346280"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346281/SRR3346281"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346282/SRR3346282"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346283/SRR3346283"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346284/SRR3346284"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346285/SRR3346285"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346286/SRR3346286"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346287/SRR3346287"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346288/SRR3346288"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346289/SRR3346289"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346290/SRR3346290"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346291/SRR3346291"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346292/SRR3346292"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346293/SRR3346293"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346294/SRR3346294"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346295/SRR3346295"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346296/SRR3346296"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346297/SRR3346297"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346298/SRR3346298"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346299/SRR3346299"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346300/SRR3346300"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346301/SRR3346301"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346302/SRR3346302"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346303/SRR3346303"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346304/SRR3346304"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346305/SRR3346305"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346306/SRR3346306"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346307/SRR3346307"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346308/SRR3346308"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346309/SRR3346309"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346310/SRR3346310"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346311/SRR3346311"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346312/SRR3346312"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346313/SRR3346313"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346314/SRR3346314"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346315/SRR3346315"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346316/SRR3346316"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346317/SRR3346317"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346318/SRR3346318"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346319/SRR3346319"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346320/SRR3346320"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346321/SRR3346321"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346322/SRR3346322"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346323/SRR3346323"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346324/SRR3346324"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346325/SRR3346325"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346326/SRR3346326"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346327/SRR3346327"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346328/SRR3346328"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346329/SRR3346329"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346330/SRR3346330"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346331/SRR3346331"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346332/SRR3346332"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346333/SRR3346333"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346334/SRR3346334"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346335/SRR3346335"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346336/SRR3346336"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346337/SRR3346337"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346338/SRR3346338"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346339/SRR3346339"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346340/SRR3346340"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346341/SRR3346341"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346342/SRR3346342"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346343/SRR3346343"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346344/SRR3346344"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346345/SRR3346345"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346346/SRR3346346"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346347/SRR3346347"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346348/SRR3346348"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346349/SRR3346349"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346350/SRR3346350"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346351/SRR3346351"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346352/SRR3346352"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346353/SRR3346353"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346354/SRR3346354"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346355/SRR3346355"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346356/SRR3346356"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346357/SRR3346357"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346358/SRR3346358"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346359/SRR3346359"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346360/SRR3346360"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346361/SRR3346361"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346257/SRR3346257"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346258/SRR3346258"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346259/SRR3346259"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346260/SRR3346260"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346261/SRR3346261"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346264/SRR3346264"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346262/SRR3346262"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346263/SRR3346263"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346265/SRR3346265"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346266/SRR3346266"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346267/SRR3346267"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346269/SRR3346269"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346270/SRR3346270"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346268/SRR3346268"
curl -L -O -C - "https://sra-pub-src-1.s3.amazonaws.com/SRR3346271/415_INPUT_ATTCAGAA-ATAGAGGC_L006_R1.unassigned.randomer.fastq.gz.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346272/SRR3346272"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346273/SRR3346273"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346274/SRR3346274"
curl -L -O -C - "https://sra-pub-src-1.s3.amazonaws.com/SRR3346275/417_CLIP_S55_L006_R1_001.D08fixed_417_02_POLR2G.randomer.fastq.gz.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346276/SRR3346276"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346277/SRR3346277"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346278/SRR3346278"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346279/SRR3346279"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346280/SRR3346280"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346281/SRR3346281"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346282/SRR3346282"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346284/SRR3346284"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346285/SRR3346285"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346283/SRR3346283"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346286/SRR3346286"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346287/SRR3346287"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346288/SRR3346288"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346289/SRR3346289"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346290/SRR3346290"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346291/SRR3346291"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346292/SRR3346292"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346293/SRR3346293"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346294/SRR3346294"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346295/SRR3346295"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346296/SRR3346296"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346299/SRR3346299"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346300/SRR3346300"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346297/SRR3346297"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346298/SRR3346298"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346301/SRR3346301"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346302/SRR3346302"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346304/SRR3346304"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346305/SRR3346305"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346303/SRR3346303"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346306/SRR3346306"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346307/SRR3346307"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346308/SRR3346308"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346309/SRR3346309"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346310/SRR3346310"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346311/SRR3346311"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346312/SRR3346312"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346314/SRR3346314"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346315/SRR3346315"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346313/SRR3346313"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346316/SRR3346316"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346319/SRR3346319"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346317/SRR3346317"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346318/SRR3346318"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346320/SRR3346320"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346321/SRR3346321"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346322/SRR3346322"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346323/SRR3346323"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346324/SRR3346324"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346325/SRR3346325"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346326/SRR3346326"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346327/SRR3346327"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346328/SRR3346328"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346329/SRR3346329"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346330/SRR3346330"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346331/SRR3346331"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346332/SRR3346332"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346333/SRR3346333"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346334/SRR3346334"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346335/SRR3346335"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346334/SRR3346334"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346336/SRR3346336"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346339/SRR3346339"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346337/SRR3346337"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346338/SRR3346338"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346340/SRR3346340"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346341/SRR3346341"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346342/SRR3346342"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346344/SRR3346344"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346345/SRR3346345"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346343/SRR3346343"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346346/SRR3346346"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346349/SRR3346349"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346347/SRR3346347"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346348/SRR3346348"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346350/SRR3346350"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346351/SRR3346351"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346352/SRR3346352"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346354/SRR3346354"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346355/SRR3346355"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346353/SRR3346353"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346353/SRR3346353"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346356/SRR3346356"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346357/SRR3346357"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346358/SRR3346358"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346359/SRR3346359"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346360/SRR3346360"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3346361/SRR3346361"

echo "Download complete. Files saved to $OUTDIR"