#!/usr/bin/env bash
# Bulk download script for GSE88722
# Generated from Yeo Lab Publications Database
# Total files: 141

OUTDIR="GSE88722"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88722/suppl/GSE88722_RAW.tar" -O "GSE88722_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 "SRR4422754"
gz1="$(_compress_if_exists 'SRR4422754_1' || true)"
gz2="$(_compress_if_exists 'SRR4422754_2' || true)"
gzs="$(_compress_if_exists 'SRR4422754' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG1_CLIP_S39_L003_R1_001.A01_TAG1_CLIP_HNRNPC.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG1_CLIP_S39_L003_R2_001.A01_TAG1_CLIP_HNRNPC.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422755"
gz1="$(_compress_if_exists 'SRR4422755_1' || true)"
gz2="$(_compress_if_exists 'SRR4422755_2' || true)"
gzs="$(_compress_if_exists 'SRR4422755' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG1_CLIP_S39_L003_R1_001.B06_TAG1_CLIP_HNRNPC.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG1_CLIP_S39_L003_R2_001.B06_TAG1_CLIP_HNRNPC.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422756"
gz1="$(_compress_if_exists 'SRR4422756_1' || true)"
gz2="$(_compress_if_exists 'SRR4422756_2' || true)"
gzs="$(_compress_if_exists 'SRR4422756' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG1_INPUT_S36_L003_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG1_INPUT_S36_L003_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422757"
gz1="$(_compress_if_exists 'SRR4422757_1' || true)"
gz2="$(_compress_if_exists 'SRR4422757_2' || true)"
gzs="$(_compress_if_exists 'SRR4422757' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG2_CLIP_S40_L003_R1_001.C01_TAG2_CLIP_CDbarcodes_HNRNPC.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG2_CLIP_S40_L003_R2_001.C01_TAG2_CLIP_CDbarcodes_HNRNPC.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422758"
gz1="$(_compress_if_exists 'SRR4422758_1' || true)"
gz2="$(_compress_if_exists 'SRR4422758_2' || true)"
gzs="$(_compress_if_exists 'SRR4422758' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG2_CLIP_S40_L003_R1_001.D08fixed_TAG2_CLIP_CDbarcodes_HNRNPC.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG2_CLIP_S40_L003_R2_001.D08fixed_TAG2_CLIP_CDbarcodes_HNRNPC.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422759"
gz1="$(_compress_if_exists 'SRR4422759_1' || true)"
gz2="$(_compress_if_exists 'SRR4422759_2' || true)"
gzs="$(_compress_if_exists 'SRR4422759' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG2_INPUT_S37_L003_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG2_INPUT_S37_L003_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422760"
gz1="$(_compress_if_exists 'SRR4422760_1' || true)"
gz2="$(_compress_if_exists 'SRR4422760_2' || true)"
gzs="$(_compress_if_exists 'SRR4422760' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG3_CLIP_S41_L003_R1_001.C01_TAG3_CLIP_HNRNPC.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG3_CLIP_S41_L003_R2_001.C01_TAG3_CLIP_HNRNPC.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422761"
gz1="$(_compress_if_exists 'SRR4422761_1' || true)"
gz2="$(_compress_if_exists 'SRR4422761_2' || true)"
gzs="$(_compress_if_exists 'SRR4422761' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG3_CLIP_S41_L003_R1_001.D08fixed_TAG3_CLIP_HNRNPC.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG3_CLIP_S41_L003_R2_001.D08fixed_TAG3_CLIP_HNRNPC.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422762"
gz1="$(_compress_if_exists 'SRR4422762_1' || true)"
gz2="$(_compress_if_exists 'SRR4422762_2' || true)"
gzs="$(_compress_if_exists 'SRR4422762' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG3_INPUT_S38_L003_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG3_INPUT_S38_L003_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422763"
gz1="$(_compress_if_exists 'SRR4422763_1' || true)"
gz2="$(_compress_if_exists 'SRR4422763_2' || true)"
gzs="$(_compress_if_exists 'SRR4422763' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG5_CLIP_S45_L003_R1_001.A01_TAG5_CLIP_FMR1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG5_CLIP_S45_L003_R2_001.A01_TAG5_CLIP_FMR1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422764"
gz1="$(_compress_if_exists 'SRR4422764_1' || true)"
gz2="$(_compress_if_exists 'SRR4422764_2' || true)"
gzs="$(_compress_if_exists 'SRR4422764' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG5_CLIP_S45_L003_R1_001.B06_TAG5_CLIP_FMR1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG5_CLIP_S45_L003_R2_001.B06_TAG5_CLIP_FMR1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422765"
gz1="$(_compress_if_exists 'SRR4422765_1' || true)"
gz2="$(_compress_if_exists 'SRR4422765_2' || true)"
gzs="$(_compress_if_exists 'SRR4422765' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG5_INPUT_S44_L003_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG5_INPUT_S44_L003_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422766"
gz1="$(_compress_if_exists 'SRR4422766_1' || true)"
gz2="$(_compress_if_exists 'SRR4422766_2' || true)"
gzs="$(_compress_if_exists 'SRR4422766' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG6_CLIP_S47_L003_R1_001.C01_TAG6_CLIP_FMR1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG6_CLIP_S47_L003_R2_001.C01_TAG6_CLIP_FMR1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422767"
gz1="$(_compress_if_exists 'SRR4422767_1' || true)"
gz2="$(_compress_if_exists 'SRR4422767_2' || true)"
gzs="$(_compress_if_exists 'SRR4422767' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG6_CLIP_S47_L003_R1_001.D08fixed_TAG6_CLIP_FMR1.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG6_CLIP_S47_L003_R2_001.D08fixed_TAG6_CLIP_FMR1.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422768"
gz1="$(_compress_if_exists 'SRR4422768_1' || true)"
gz2="$(_compress_if_exists 'SRR4422768_2' || true)"
gzs="$(_compress_if_exists 'SRR4422768' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG6_INPUT_S46_L003_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG6_INPUT_S46_L003_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422769"
gz1="$(_compress_if_exists 'SRR4422769_1' || true)"
gz2="$(_compress_if_exists 'SRR4422769_2' || true)"
gzs="$(_compress_if_exists 'SRR4422769' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG10_CLIP_S25_L005_R1_001.A01_TAG10_CLIP_RBFOX2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG10_CLIP_S25_L005_R2_001.A01_TAG10_CLIP_RBFOX2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422770"
gz1="$(_compress_if_exists 'SRR4422770_1' || true)"
gz2="$(_compress_if_exists 'SRR4422770_2' || true)"
gzs="$(_compress_if_exists 'SRR4422770' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG10_CLIP_S25_L005_R1_001.B06_TAG10_CLIP_RBFOX2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG10_CLIP_S25_L005_R2_001.B06_TAG10_CLIP_RBFOX2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422771"
gz1="$(_compress_if_exists 'SRR4422771_1' || true)"
gz2="$(_compress_if_exists 'SRR4422771_2' || true)"
gzs="$(_compress_if_exists 'SRR4422771' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG10_INPUT_S22_L005_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG10_INPUT_S22_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422772"
gz1="$(_compress_if_exists 'SRR4422772_1' || true)"
gz2="$(_compress_if_exists 'SRR4422772_2' || true)"
gzs="$(_compress_if_exists 'SRR4422772' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG12_CLIP_S27_L005_R1_001.C01_TAG12_CLIP_RBFOX2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG12_CLIP_S27_L005_R2_001.C01_TAG12_CLIP_RBFOX2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422773"
gz1="$(_compress_if_exists 'SRR4422773_1' || true)"
gz2="$(_compress_if_exists 'SRR4422773_2' || true)"
gzs="$(_compress_if_exists 'SRR4422773' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG12_CLIP_S27_L005_R1_001.D08fixed_TAG12_CLIP_RBFOX2.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG12_CLIP_S27_L005_R2_001.D08fixed_TAG12_CLIP_RBFOX2.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422774"
gz1="$(_compress_if_exists 'SRR4422774_1' || true)"
gz2="$(_compress_if_exists 'SRR4422774_2' || true)"
gzs="$(_compress_if_exists 'SRR4422774' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG12_INPUT_S24_L005_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG12_INPUT_S24_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422775"
gz1="$(_compress_if_exists 'SRR4422775_1' || true)"
gz2="$(_compress_if_exists 'SRR4422775_2' || true)"
gzs="$(_compress_if_exists 'SRR4422775' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG13_CLIP_S35_L002_R1_001.A01_TAG13_CLIP_LIN28B.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG13_CLIP_S35_L002_R2_001.A01_TAG13_CLIP_LIN28B.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422776"
gz1="$(_compress_if_exists 'SRR4422776_1' || true)"
gz2="$(_compress_if_exists 'SRR4422776_2' || true)"
gzs="$(_compress_if_exists 'SRR4422776' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG13_CLIP_S35_L002_R1_001.B06_TAG13_CLIP_LIN28B.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG13_CLIP_S35_L002_R2_001.B06_TAG13_CLIP_LIN28B.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422777"
gz1="$(_compress_if_exists 'SRR4422777_1' || true)"
gz2="$(_compress_if_exists 'SRR4422777_2' || true)"
gzs="$(_compress_if_exists 'SRR4422777' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG13_INPUT_S28_L005_R1_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422778"
gz1="$(_compress_if_exists 'SRR4422778_1' || true)"
gz2="$(_compress_if_exists 'SRR4422778_2' || true)"
gzs="$(_compress_if_exists 'SRR4422778' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG13_INPUT_S28_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422779"
gz1="$(_compress_if_exists 'SRR4422779_1' || true)"
gz2="$(_compress_if_exists 'SRR4422779_2' || true)"
gzs="$(_compress_if_exists 'SRR4422779' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG14_CLIP_S30_L005_R1_001.A01_TAG14_CLIP_LIN28B.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG14_CLIP_S30_L005_R2_001.A01_TAG14_CLIP_LIN28B.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422780"
gz1="$(_compress_if_exists 'SRR4422780_1' || true)"
gz2="$(_compress_if_exists 'SRR4422780_2' || true)"
gzs="$(_compress_if_exists 'SRR4422780' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG14_CLIP_S30_L005_R1_001.B06_TAG14_CLIP_LIN28B.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG14_CLIP_S30_L005_R2_001.B06_TAG14_CLIP_LIN28B.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422781"
gz1="$(_compress_if_exists 'SRR4422781_1' || true)"
gz2="$(_compress_if_exists 'SRR4422781_2' || true)"
gzs="$(_compress_if_exists 'SRR4422781' || true)"

fasterq-dump --split-files "SRR4422782"
gz1="$(_compress_if_exists 'SRR4422782_1' || true)"
gz2="$(_compress_if_exists 'SRR4422782_2' || true)"
gzs="$(_compress_if_exists 'SRR4422782' || true)"

fasterq-dump --split-files "SRR4422783"
gz1="$(_compress_if_exists 'SRR4422783_1' || true)"
gz2="$(_compress_if_exists 'SRR4422783_2' || true)"
gzs="$(_compress_if_exists 'SRR4422783' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG15_CLIP_S32_L005_R1_001.A01_TAG15_CLIP_DGCR8.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG15_CLIP_S32_L005_R2_001.A01_TAG15_CLIP_DGCR8.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422784"
gz1="$(_compress_if_exists 'SRR4422784_1' || true)"
gz2="$(_compress_if_exists 'SRR4422784_2' || true)"
gzs="$(_compress_if_exists 'SRR4422784' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG15_CLIP_S32_L005_R1_001.B06_TAG15_CLIP_DGCR8.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG15_CLIP_S32_L005_R2_001.B06_TAG15_CLIP_DGCR8.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422785"
gz1="$(_compress_if_exists 'SRR4422785_1' || true)"
gz2="$(_compress_if_exists 'SRR4422785_2' || true)"
gzs="$(_compress_if_exists 'SRR4422785' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG15_INPUT_S31_L005_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG15_INPUT_S31_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422786"
gz1="$(_compress_if_exists 'SRR4422786_1' || true)"
gz2="$(_compress_if_exists 'SRR4422786_2' || true)"
gzs="$(_compress_if_exists 'SRR4422786' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG16_CLIP_S35_L005_R1_001.C01_TAG16_CLIP_DGCR8.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG16_CLIP_S35_L005_R2_001.C01_TAG16_CLIP_DGCR8.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422787"
gz1="$(_compress_if_exists 'SRR4422787_1' || true)"
gz2="$(_compress_if_exists 'SRR4422787_2' || true)"
gzs="$(_compress_if_exists 'SRR4422787' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG16_CLIP_S35_L005_R1_001.D08fixed_TAG16_CLIP_DGCR8.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG16_CLIP_S35_L005_R2_001.D08fixed_TAG16_CLIP_DGCR8.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422788"
gz1="$(_compress_if_exists 'SRR4422788_1' || true)"
gz2="$(_compress_if_exists 'SRR4422788_2' || true)"
gzs="$(_compress_if_exists 'SRR4422788' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TAG16_INPUT_S33_L005_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TAG16_INPUT_S33_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422789"
gz1="$(_compress_if_exists 'SRR4422789_1' || true)"
gz2="$(_compress_if_exists 'SRR4422789_2' || true)"
gzs="$(_compress_if_exists 'SRR4422789' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG1_V5_CLIP1_S53_L005_R1_001.F05_EV116_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG1_V5_CLIP1_S53_L005_R2_001.F05_EV116_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422790"
gz1="$(_compress_if_exists 'SRR4422790_1' || true)"
gz2="$(_compress_if_exists 'SRR4422790_2' || true)"
gzs="$(_compress_if_exists 'SRR4422790' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG1_V5_CLIP1_S53_L005_R1_001.A04_EV116_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG1_V5_CLIP1_S53_L005_R2_001.A04_EV116_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422791"
gz1="$(_compress_if_exists 'SRR4422791_1' || true)"
gz2="$(_compress_if_exists 'SRR4422791_2' || true)"
gzs="$(_compress_if_exists 'SRR4422791' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG2_V5_CLIP2_S54_L005_R1_001.F05_EV117_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG2_V5_CLIP2_S54_L005_R2_001.F05_EV117_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422792"
gz1="$(_compress_if_exists 'SRR4422792_1' || true)"
gz2="$(_compress_if_exists 'SRR4422792_2' || true)"
gzs="$(_compress_if_exists 'SRR4422792' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG2_V5_CLIP2_S54_L005_R1_001.A04_EV117_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG2_V5_CLIP2_S54_L005_R2_001.A04_EV117_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422793"
gz1="$(_compress_if_exists 'SRR4422793_1' || true)"
gz2="$(_compress_if_exists 'SRR4422793_2' || true)"
gzs="$(_compress_if_exists 'SRR4422793' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG3_V5_CLIP3_S55_L005_R1_001.F05_EV118_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG3_V5_CLIP3_S55_L005_R2_001.F05_EV118_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422794"
gz1="$(_compress_if_exists 'SRR4422794_1' || true)"
gz2="$(_compress_if_exists 'SRR4422794_2' || true)"
gzs="$(_compress_if_exists 'SRR4422794' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG3_V5_CLIP3_S55_L005_R1_001.A04_EV118_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG3_V5_CLIP3_S55_L005_R2_001.A04_EV118_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422795"
gz1="$(_compress_if_exists 'SRR4422795_1' || true)"
gz2="$(_compress_if_exists 'SRR4422795_2' || true)"
gzs="$(_compress_if_exists 'SRR4422795' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG4_V5_CLIP4_S56_L005_R1_001.F05_EV119_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG4_V5_CLIP4_S56_L005_R2_001.F05_EV119_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422796"
gz1="$(_compress_if_exists 'SRR4422796_1' || true)"
gz2="$(_compress_if_exists 'SRR4422796_2' || true)"
gzs="$(_compress_if_exists 'SRR4422796' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG4_V5_CLIP4_S56_L005_R1_001.A04_EV119_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG4_V5_CLIP4_S56_L005_R2_001.A04_EV119_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422797"
gz1="$(_compress_if_exists 'SRR4422797_1' || true)"
gz2="$(_compress_if_exists 'SRR4422797_2' || true)"
gzs="$(_compress_if_exists 'SRR4422797' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG5_V5_CLIP5_S64_L006_R1_001.F05_EV120_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG5_V5_CLIP5_S64_L006_R2_001.F05_EV120_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422798"
gz1="$(_compress_if_exists 'SRR4422798_1' || true)"
gz2="$(_compress_if_exists 'SRR4422798_2' || true)"
gzs="$(_compress_if_exists 'SRR4422798' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG5_V5_CLIP5_S64_L006_R1_001.A04_EV120_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG5_V5_CLIP5_S64_L006_R2_001.A04_EV120_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422799"
gz1="$(_compress_if_exists 'SRR4422799_1' || true)"
gz2="$(_compress_if_exists 'SRR4422799_2' || true)"
gzs="$(_compress_if_exists 'SRR4422799' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG6_V5_CLIP6_S65_L006_R1_001.F05_EV121_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG6_V5_CLIP6_S65_L006_R2_001.F05_EV121_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422800"
gz1="$(_compress_if_exists 'SRR4422800_1' || true)"
gz2="$(_compress_if_exists 'SRR4422800_2' || true)"
gzs="$(_compress_if_exists 'SRR4422800' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG6_V5_CLIP6_S65_L006_R1_001.A04_EV121_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG6_V5_CLIP6_S65_L006_R2_001.A04_EV121_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422801"
gz1="$(_compress_if_exists 'SRR4422801_1' || true)"
gz2="$(_compress_if_exists 'SRR4422801_2' || true)"
gzs="$(_compress_if_exists 'SRR4422801' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG7_V5_CLIP7_S66_L006_R1_001.F05_EV122_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG7_V5_CLIP7_S66_L006_R2_001.F05_EV122_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422802"
gz1="$(_compress_if_exists 'SRR4422802_1' || true)"
gz2="$(_compress_if_exists 'SRR4422802_2' || true)"
gzs="$(_compress_if_exists 'SRR4422802' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG7_V5_CLIP7_S66_L006_R1_001.A04_EV122_FLAG_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG7_V5_CLIP7_S66_L006_R2_001.A04_EV122_FLAG_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422803"
gz1="$(_compress_if_exists 'SRR4422803_1' || true)"
gz2="$(_compress_if_exists 'SRR4422803_2' || true)"
gzs="$(_compress_if_exists 'SRR4422803' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG1_V5_CLIP1_S53_L005_R1_001.A03_EV116_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG1_V5_CLIP1_S53_L005_R2_001.A03_EV116_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422804"
gz1="$(_compress_if_exists 'SRR4422804_1' || true)"
gz2="$(_compress_if_exists 'SRR4422804_2' || true)"
gzs="$(_compress_if_exists 'SRR4422804' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG1_V5_CLIP1_S53_L005_R1_001.G07_EV116_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG1_V5_CLIP1_S53_L005_R2_001.G07_EV116_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422805"
gz1="$(_compress_if_exists 'SRR4422805_1' || true)"
gz2="$(_compress_if_exists 'SRR4422805_2' || true)"
gzs="$(_compress_if_exists 'SRR4422805' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG2_V5_CLIP2_S54_L005_R1_001.A03_EV117_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG2_V5_CLIP2_S54_L005_R2_001.A03_EV117_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422806"
gz1="$(_compress_if_exists 'SRR4422806_1' || true)"
gz2="$(_compress_if_exists 'SRR4422806_2' || true)"
gzs="$(_compress_if_exists 'SRR4422806' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG2_V5_CLIP2_S54_L005_R1_001.G07_EV117_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG2_V5_CLIP2_S54_L005_R2_001.G07_EV117_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422807"
gz1="$(_compress_if_exists 'SRR4422807_1' || true)"
gz2="$(_compress_if_exists 'SRR4422807_2' || true)"
gzs="$(_compress_if_exists 'SRR4422807' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG3_V5_CLIP3_S55_L005_R1_001.A03_EV118_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG3_V5_CLIP3_S55_L005_R2_001.A03_EV118_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422808"
gz1="$(_compress_if_exists 'SRR4422808_1' || true)"
gz2="$(_compress_if_exists 'SRR4422808_2' || true)"
gzs="$(_compress_if_exists 'SRR4422808' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG3_V5_CLIP3_S55_L005_R1_001.G07_EV118_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG3_V5_CLIP3_S55_L005_R2_001.G07_EV118_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422809"
gz1="$(_compress_if_exists 'SRR4422809_1' || true)"
gz2="$(_compress_if_exists 'SRR4422809_2' || true)"
gzs="$(_compress_if_exists 'SRR4422809' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG4_V5_CLIP4_S56_L005_R1_001.A03_EV119_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG4_V5_CLIP4_S56_L005_R2_001.A03_EV119_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422810"
gz1="$(_compress_if_exists 'SRR4422810_1' || true)"
gz2="$(_compress_if_exists 'SRR4422810_2' || true)"
gzs="$(_compress_if_exists 'SRR4422810' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG4_V5_CLIP4_S56_L005_R1_001.G07_EV119_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG4_V5_CLIP4_S56_L005_R2_001.G07_EV119_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422811"
gz1="$(_compress_if_exists 'SRR4422811_1' || true)"
gz2="$(_compress_if_exists 'SRR4422811_2' || true)"
gzs="$(_compress_if_exists 'SRR4422811' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG5_V5_CLIP5_S64_L006_R1_001.A03_EV120_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG5_V5_CLIP5_S64_L006_R2_001.A03_EV120_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422812"
gz1="$(_compress_if_exists 'SRR4422812_1' || true)"
gz2="$(_compress_if_exists 'SRR4422812_2' || true)"
gzs="$(_compress_if_exists 'SRR4422812' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG5_V5_CLIP5_S64_L006_R1_001.G07_EV120_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG5_V5_CLIP5_S64_L006_R2_001.G07_EV120_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422813"
gz1="$(_compress_if_exists 'SRR4422813_1' || true)"
gz2="$(_compress_if_exists 'SRR4422813_2' || true)"
gzs="$(_compress_if_exists 'SRR4422813' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG6_V5_CLIP6_S65_L006_R1_001.A03_EV121_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG6_V5_CLIP6_S65_L006_R2_001.A03_EV121_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422814"
gz1="$(_compress_if_exists 'SRR4422814_1' || true)"
gz2="$(_compress_if_exists 'SRR4422814_2' || true)"
gzs="$(_compress_if_exists 'SRR4422814' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG6_V5_CLIP6_S65_L006_R1_001.G07_EV121_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG6_V5_CLIP6_S65_L006_R2_001.G07_EV121_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422815"
gz1="$(_compress_if_exists 'SRR4422815_1' || true)"
gz2="$(_compress_if_exists 'SRR4422815_2' || true)"
gzs="$(_compress_if_exists 'SRR4422815' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG7_V5_CLIP7_S66_L006_R1_001.A03_EV122_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG7_V5_CLIP7_S66_L006_R2_001.A03_EV122_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422816"
gz1="$(_compress_if_exists 'SRR4422816_1' || true)"
gz2="$(_compress_if_exists 'SRR4422816_2' || true)"
gzs="$(_compress_if_exists 'SRR4422816' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_FLAG7_V5_CLIP7_S66_L006_R1_001.G07_EV122_V5_none.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_FLAG7_V5_CLIP7_S66_L006_R2_001.G07_EV122_V5_none.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422817"
gz1="$(_compress_if_exists 'SRR4422817_1' || true)"
gz2="$(_compress_if_exists 'SRR4422817_2' || true)"
gzs="$(_compress_if_exists 'SRR4422817' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_IN1_S49_L005_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_IN1_S49_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422818"
gz1="$(_compress_if_exists 'SRR4422818_1' || true)"
gz2="$(_compress_if_exists 'SRR4422818_2' || true)"
gzs="$(_compress_if_exists 'SRR4422818' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_IN2_S50_L005_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_IN2_S50_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422819"
gz1="$(_compress_if_exists 'SRR4422819_1' || true)"
gz2="$(_compress_if_exists 'SRR4422819_2' || true)"
gzs="$(_compress_if_exists 'SRR4422819' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_IN3_S51_L005_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_IN3_S51_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422820"
gz1="$(_compress_if_exists 'SRR4422820_1' || true)"
gz2="$(_compress_if_exists 'SRR4422820_2' || true)"
gzs="$(_compress_if_exists 'SRR4422820' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_IN4_S52_L005_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_IN4_S52_L005_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422821"
gz1="$(_compress_if_exists 'SRR4422821_1' || true)"
gz2="$(_compress_if_exists 'SRR4422821_2' || true)"
gzs="$(_compress_if_exists 'SRR4422821' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_IN5_S61_L006_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_IN5_S61_L006_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422822"
gz1="$(_compress_if_exists 'SRR4422822_1' || true)"
gz2="$(_compress_if_exists 'SRR4422822_2' || true)"
gzs="$(_compress_if_exists 'SRR4422822' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_IN6_S62_L006_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_IN6_S62_L006_R2_001.unassigned.randomer.fastq.gz"
fi

fasterq-dump --split-files "SRR4422823"
gz1="$(_compress_if_exists 'SRR4422823_1' || true)"
gz2="$(_compress_if_exists 'SRR4422823_2' || true)"
gzs="$(_compress_if_exists 'SRR4422823' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "293T_IN7_S63_L006_R1_001.unassigned.randomer.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "293T_IN7_S63_L006_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/SRR4422754/SRR4422754"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422755/SRR4422755"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422756/SRR4422756"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422757/SRR4422757"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422758/SRR4422758"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422759/SRR4422759"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422760/SRR4422760"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422761/SRR4422761"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422762/SRR4422762"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422763/SRR4422763"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422764/SRR4422764"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422765/SRR4422765"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422766/SRR4422766"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422767/SRR4422767"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422768/SRR4422768"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422769/SRR4422769"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422770/SRR4422770"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422771/SRR4422771"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422772/SRR4422772"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422773/SRR4422773"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422774/SRR4422774"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422775/SRR4422775"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422776/SRR4422776"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422777/SRR4422777"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422778/SRR4422778"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422779/SRR4422779"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422780/SRR4422780"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422781/SRR4422781"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422782/SRR4422782"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422783/SRR4422783"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422784/SRR4422784"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422785/SRR4422785"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422786/SRR4422786"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422787/SRR4422787"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422788/SRR4422788"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422789/SRR4422789"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422790/SRR4422790"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422791/SRR4422791"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422792/SRR4422792"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422793/SRR4422793"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422794/SRR4422794"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422795/SRR4422795"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422796/SRR4422796"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422797/SRR4422797"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422798/SRR4422798"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422799/SRR4422799"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422800/SRR4422800"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422801/SRR4422801"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422802/SRR4422802"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422803/SRR4422803"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422804/SRR4422804"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422805/SRR4422805"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422806/SRR4422806"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422807/SRR4422807"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422808/SRR4422808"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422809/SRR4422809"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422810/SRR4422810"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422811/SRR4422811"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422812/SRR4422812"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422813/SRR4422813"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422814/SRR4422814"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422815/SRR4422815"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422816/SRR4422816"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422817/SRR4422817"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422818/SRR4422818"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422819/SRR4422819"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422820/SRR4422820"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422821/SRR4422821"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422822/SRR4422822"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422823/SRR4422823"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422803/SRR4422803"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422790/SRR4422790"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422789/SRR4422789"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422804/SRR4422804"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422805/SRR4422805"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422792/SRR4422792"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422791/SRR4422791"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422806/SRR4422806"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422807/SRR4422807"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422794/SRR4422794"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422793/SRR4422793"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422808/SRR4422808"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422809/SRR4422809"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422796/SRR4422796"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422795/SRR4422795"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422810/SRR4422810"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422811/SRR4422811"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422798/SRR4422798"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422797/SRR4422797"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422812/SRR4422812"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422813/SRR4422813"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422800/SRR4422800"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422799/SRR4422799"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422814/SRR4422814"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422815/SRR4422815"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422802/SRR4422802"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422801/SRR4422801"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422816/SRR4422816"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422817/SRR4422817"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422818/SRR4422818"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422819/SRR4422819"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422820/SRR4422820"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422821/SRR4422821"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422822/SRR4422822"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422823/SRR4422823"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422781/SRR4422781"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422782/SRR4422782"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422769/SRR4422769"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422770/SRR4422770"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422771/SRR4422771"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422772/SRR4422772"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422773/SRR4422773"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422774/SRR4422774"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422775/SRR4422775"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422776/SRR4422776"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422777/SRR4422777"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422778/SRR4422778"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422779/SRR4422779"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422780/SRR4422780"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422783/SRR4422783"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422784/SRR4422784"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422785/SRR4422785"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422786/SRR4422786"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422787/SRR4422787"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422788/SRR4422788"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422754/SRR4422754"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422755/SRR4422755"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422756/SRR4422756"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422757/SRR4422757"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422758/SRR4422758"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422759/SRR4422759"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422760/SRR4422760"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422761/SRR4422761"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422762/SRR4422762"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422763/SRR4422763"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422764/SRR4422764"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422765/SRR4422765"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422766/SRR4422766"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422767/SRR4422767"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR4422768/SRR4422768"

echo "Download complete. Files saved to $OUTDIR"