#!/usr/bin/env bash
# Bulk download script for GSE240014
# Generated from Yeo Lab Publications Database
# Total files: 124

OUTDIR="GSE240014"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ANonly_FM_cleaned_confident_peaks.bed.gz" -O "GSE240014_ANonly_FM_cleaned_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ANonly_FM_confident_peaks.bed.gz" -O "GSE240014_ANonly_FM_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ANonly_cleaned_confident_peaks.bed.gz" -O "GSE240014_ANonly_cleaned_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ANonly_confident_peaks.bed.gz" -O "GSE240014_ANonly_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_Bufferonly_FM_confident_peaks.bed.gz" -O "GSE240014_Bufferonly_FM_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_Bufferonly_confident_peaks.bed.gz" -O "GSE240014_Bufferonly_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ME_ANonly_cleaned_confident_peaks.bed.gz" -O "GSE240014_ME_ANonly_cleaned_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ME_ANonly_confident_peaks.bed.gz" -O "GSE240014_ME_ANonly_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ME_Bufferonly_confident_peaks.bed.gz" -O "GSE240014_ME_Bufferonly_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ME_RBFOX2_cleaned_confident_peaks.bed.gz" -O "GSE240014_ME_RBFOX2_cleaned_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_ME_RBFOX2_confident_peaks.bed.gz" -O "GSE240014_ME_RBFOX2_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_RAW.tar" -O "GSE240014_RAW.tar"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_RBFOX2_FM_cleaned_confident_peaks.bed.gz" -O "GSE240014_RBFOX2_FM_cleaned_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_RBFOX2_FM_confident_peaks.bed.gz" -O "GSE240014_RBFOX2_FM_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_RBFOX2_cleaned_confident_peaks.bed.gz" -O "GSE240014_RBFOX2_cleaned_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_RBFOX2_confident_peaks.bed.gz" -O "GSE240014_RBFOX2_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_TDP43_FM_cleaned_confident_peaks.bed.gz" -O "GSE240014_TDP43_FM_cleaned_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_TDP43_FM_confident_peaks.bed.gz" -O "GSE240014_TDP43_FM_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_TDP43_cleaned_confident_peaks.bed.gz" -O "GSE240014_TDP43_cleaned_confident_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240014/suppl/GSE240014_TDP43_confident_peaks.bed.gz" -O "GSE240014_TDP43_confident_peaks.bed.gz"

# --- 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 "SRR25508725"
gz1="$(_compress_if_exists 'SRR25508725_1' || true)"
gz2="$(_compress_if_exists 'SRR25508725_2' || true)"
gzs="$(_compress_if_exists 'SRR25508725' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP08_14_S14_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508726"
gz1="$(_compress_if_exists 'SRR25508726_1' || true)"
gz2="$(_compress_if_exists 'SRR25508726_2' || true)"
gzs="$(_compress_if_exists 'SRR25508726' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP08_13_S13_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508727"
gz1="$(_compress_if_exists 'SRR25508727_1' || true)"
gz2="$(_compress_if_exists 'SRR25508727_2' || true)"
gzs="$(_compress_if_exists 'SRR25508727' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP08_12_S12_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508728"
gz1="$(_compress_if_exists 'SRR25508728_1' || true)"
gz2="$(_compress_if_exists 'SRR25508728_2' || true)"
gzs="$(_compress_if_exists 'SRR25508728' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP08_11_S11_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508729"
gz1="$(_compress_if_exists 'SRR25508729_1' || true)"
gz2="$(_compress_if_exists 'SRR25508729_2' || true)"
gzs="$(_compress_if_exists 'SRR25508729' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP08_10_S10_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508730"
gz1="$(_compress_if_exists 'SRR25508730_1' || true)"
gz2="$(_compress_if_exists 'SRR25508730_2' || true)"
gzs="$(_compress_if_exists 'SRR25508730' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP08_09_S9_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508731"
gz1="$(_compress_if_exists 'SRR25508731_1' || true)"
gz2="$(_compress_if_exists 'SRR25508731_2' || true)"
gzs="$(_compress_if_exists 'SRR25508731' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-09_S9_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508732"
gz1="$(_compress_if_exists 'SRR25508732_1' || true)"
gz2="$(_compress_if_exists 'SRR25508732_2' || true)"
gzs="$(_compress_if_exists 'SRR25508732' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-09_S9_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508733"
gz1="$(_compress_if_exists 'SRR25508733_1' || true)"
gz2="$(_compress_if_exists 'SRR25508733_2' || true)"
gzs="$(_compress_if_exists 'SRR25508733' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-08_S8_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508734"
gz1="$(_compress_if_exists 'SRR25508734_1' || true)"
gz2="$(_compress_if_exists 'SRR25508734_2' || true)"
gzs="$(_compress_if_exists 'SRR25508734' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-08_S8_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508735"
gz1="$(_compress_if_exists 'SRR25508735_1' || true)"
gz2="$(_compress_if_exists 'SRR25508735_2' || true)"
gzs="$(_compress_if_exists 'SRR25508735' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-07_S7_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508736"
gz1="$(_compress_if_exists 'SRR25508736_1' || true)"
gz2="$(_compress_if_exists 'SRR25508736_2' || true)"
gzs="$(_compress_if_exists 'SRR25508736' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-07_S7_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508737"
gz1="$(_compress_if_exists 'SRR25508737_1' || true)"
gz2="$(_compress_if_exists 'SRR25508737_2' || true)"
gzs="$(_compress_if_exists 'SRR25508737' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-06_S6_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508738"
gz1="$(_compress_if_exists 'SRR25508738_1' || true)"
gz2="$(_compress_if_exists 'SRR25508738_2' || true)"
gzs="$(_compress_if_exists 'SRR25508738' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-06_S6_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508739"
gz1="$(_compress_if_exists 'SRR25508739_1' || true)"
gz2="$(_compress_if_exists 'SRR25508739_2' || true)"
gzs="$(_compress_if_exists 'SRR25508739' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-05_S5_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508740"
gz1="$(_compress_if_exists 'SRR25508740_1' || true)"
gz2="$(_compress_if_exists 'SRR25508740_2' || true)"
gzs="$(_compress_if_exists 'SRR25508740' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-05_S5_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508741"
gz1="$(_compress_if_exists 'SRR25508741_1' || true)"
gz2="$(_compress_if_exists 'SRR25508741_2' || true)"
gzs="$(_compress_if_exists 'SRR25508741' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-04_S4_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508742"
gz1="$(_compress_if_exists 'SRR25508742_1' || true)"
gz2="$(_compress_if_exists 'SRR25508742_2' || true)"
gzs="$(_compress_if_exists 'SRR25508742' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-04_S4_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508743"
gz1="$(_compress_if_exists 'SRR25508743_1' || true)"
gz2="$(_compress_if_exists 'SRR25508743_2' || true)"
gzs="$(_compress_if_exists 'SRR25508743' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-03_S3_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508744"
gz1="$(_compress_if_exists 'SRR25508744_1' || true)"
gz2="$(_compress_if_exists 'SRR25508744_2' || true)"
gzs="$(_compress_if_exists 'SRR25508744' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-03_S3_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508745"
gz1="$(_compress_if_exists 'SRR25508745_1' || true)"
gz2="$(_compress_if_exists 'SRR25508745_2' || true)"
gzs="$(_compress_if_exists 'SRR25508745' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-02_S2_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508746"
gz1="$(_compress_if_exists 'SRR25508746_1' || true)"
gz2="$(_compress_if_exists 'SRR25508746_2' || true)"
gzs="$(_compress_if_exists 'SRR25508746' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-02_S2_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508747"
gz1="$(_compress_if_exists 'SRR25508747_1' || true)"
gz2="$(_compress_if_exists 'SRR25508747_2' || true)"
gzs="$(_compress_if_exists 'SRR25508747' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-01_S1_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508748"
gz1="$(_compress_if_exists 'SRR25508748_1' || true)"
gz2="$(_compress_if_exists 'SRR25508748_2' || true)"
gzs="$(_compress_if_exists 'SRR25508748' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP12-01_S1_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508749"
gz1="$(_compress_if_exists 'SRR25508749_1' || true)"
gz2="$(_compress_if_exists 'SRR25508749_2' || true)"
gzs="$(_compress_if_exists 'SRR25508749' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_36_S36_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508750"
gz1="$(_compress_if_exists 'SRR25508750_1' || true)"
gz2="$(_compress_if_exists 'SRR25508750_2' || true)"
gzs="$(_compress_if_exists 'SRR25508750' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_36_S60_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508751"
gz1="$(_compress_if_exists 'SRR25508751_1' || true)"
gz2="$(_compress_if_exists 'SRR25508751_2' || true)"
gzs="$(_compress_if_exists 'SRR25508751' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_36_S60_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508752"
gz1="$(_compress_if_exists 'SRR25508752_1' || true)"
gz2="$(_compress_if_exists 'SRR25508752_2' || true)"
gzs="$(_compress_if_exists 'SRR25508752' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_35_S35_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508753"
gz1="$(_compress_if_exists 'SRR25508753_1' || true)"
gz2="$(_compress_if_exists 'SRR25508753_2' || true)"
gzs="$(_compress_if_exists 'SRR25508753' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_34_S34_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508754"
gz1="$(_compress_if_exists 'SRR25508754_1' || true)"
gz2="$(_compress_if_exists 'SRR25508754_2' || true)"
gzs="$(_compress_if_exists 'SRR25508754' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_33_S33_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508755"
gz1="$(_compress_if_exists 'SRR25508755_1' || true)"
gz2="$(_compress_if_exists 'SRR25508755_2' || true)"
gzs="$(_compress_if_exists 'SRR25508755' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_32_S32_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508756"
gz1="$(_compress_if_exists 'SRR25508756_1' || true)"
gz2="$(_compress_if_exists 'SRR25508756_2' || true)"
gzs="$(_compress_if_exists 'SRR25508756' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_31_S31_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508757"
gz1="$(_compress_if_exists 'SRR25508757_1' || true)"
gz2="$(_compress_if_exists 'SRR25508757_2' || true)"
gzs="$(_compress_if_exists 'SRR25508757' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_27_S27_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508758"
gz1="$(_compress_if_exists 'SRR25508758_1' || true)"
gz2="$(_compress_if_exists 'SRR25508758_2' || true)"
gzs="$(_compress_if_exists 'SRR25508758' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_26_S26_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508759"
gz1="$(_compress_if_exists 'SRR25508759_1' || true)"
gz2="$(_compress_if_exists 'SRR25508759_2' || true)"
gzs="$(_compress_if_exists 'SRR25508759' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_21_S21_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508760"
gz1="$(_compress_if_exists 'SRR25508760_1' || true)"
gz2="$(_compress_if_exists 'SRR25508760_2' || true)"
gzs="$(_compress_if_exists 'SRR25508760' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_25_S25_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508761"
gz1="$(_compress_if_exists 'SRR25508761_1' || true)"
gz2="$(_compress_if_exists 'SRR25508761_2' || true)"
gzs="$(_compress_if_exists 'SRR25508761' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_25_S59_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508762"
gz1="$(_compress_if_exists 'SRR25508762_1' || true)"
gz2="$(_compress_if_exists 'SRR25508762_2' || true)"
gzs="$(_compress_if_exists 'SRR25508762' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_25_S59_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508763"
gz1="$(_compress_if_exists 'SRR25508763_1' || true)"
gz2="$(_compress_if_exists 'SRR25508763_2' || true)"
gzs="$(_compress_if_exists 'SRR25508763' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_20_S20_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508764"
gz1="$(_compress_if_exists 'SRR25508764_1' || true)"
gz2="$(_compress_if_exists 'SRR25508764_2' || true)"
gzs="$(_compress_if_exists 'SRR25508764' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_19_S19_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508765"
gz1="$(_compress_if_exists 'SRR25508765_1' || true)"
gz2="$(_compress_if_exists 'SRR25508765_2' || true)"
gzs="$(_compress_if_exists 'SRR25508765' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_18_S18_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508766"
gz1="$(_compress_if_exists 'SRR25508766_1' || true)"
gz2="$(_compress_if_exists 'SRR25508766_2' || true)"
gzs="$(_compress_if_exists 'SRR25508766' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_17_S17_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508767"
gz1="$(_compress_if_exists 'SRR25508767_1' || true)"
gz2="$(_compress_if_exists 'SRR25508767_2' || true)"
gzs="$(_compress_if_exists 'SRR25508767' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_16_S16_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508768"
gz1="$(_compress_if_exists 'SRR25508768_1' || true)"
gz2="$(_compress_if_exists 'SRR25508768_2' || true)"
gzs="$(_compress_if_exists 'SRR25508768' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_15_S15_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508769"
gz1="$(_compress_if_exists 'SRR25508769_1' || true)"
gz2="$(_compress_if_exists 'SRR25508769_2' || true)"
gzs="$(_compress_if_exists 'SRR25508769' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_14_S14_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508770"
gz1="$(_compress_if_exists 'SRR25508770_1' || true)"
gz2="$(_compress_if_exists 'SRR25508770_2' || true)"
gzs="$(_compress_if_exists 'SRR25508770' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_13_S13_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508771"
gz1="$(_compress_if_exists 'SRR25508771_1' || true)"
gz2="$(_compress_if_exists 'SRR25508771_2' || true)"
gzs="$(_compress_if_exists 'SRR25508771' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_09_S9_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508772"
gz1="$(_compress_if_exists 'SRR25508772_1' || true)"
gz2="$(_compress_if_exists 'SRR25508772_2' || true)"
gzs="$(_compress_if_exists 'SRR25508772' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_08_S8_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508773"
gz1="$(_compress_if_exists 'SRR25508773_1' || true)"
gz2="$(_compress_if_exists 'SRR25508773_2' || true)"
gzs="$(_compress_if_exists 'SRR25508773' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_07_S7_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508774"
gz1="$(_compress_if_exists 'SRR25508774_1' || true)"
gz2="$(_compress_if_exists 'SRR25508774_2' || true)"
gzs="$(_compress_if_exists 'SRR25508774' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_03_S3_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508775"
gz1="$(_compress_if_exists 'SRR25508775_1' || true)"
gz2="$(_compress_if_exists 'SRR25508775_2' || true)"
gzs="$(_compress_if_exists 'SRR25508775' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_02_S2_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR25508776"
gz1="$(_compress_if_exists 'SRR25508776_1' || true)"
gz2="$(_compress_if_exists 'SRR25508776_2' || true)"
gzs="$(_compress_if_exists 'SRR25508776' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "isSTAMP10_01_S1_L004_R1_001.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508725/SRR25508725"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508726/SRR25508726"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508727/SRR25508727"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508728/SRR25508728"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508729/SRR25508729"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508730/SRR25508730"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508731/SRR25508731"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508732/SRR25508732"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508733/SRR25508733"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508734/SRR25508734"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508735/SRR25508735"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508736/SRR25508736"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508737/SRR25508737"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508738/SRR25508738"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508739/SRR25508739"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508740/SRR25508740"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508741/SRR25508741"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508742/SRR25508742"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508743/SRR25508743"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508744/SRR25508744"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508745/SRR25508745"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508746/SRR25508746"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508747/SRR25508747"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508748/SRR25508748"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508749/SRR25508749"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508750/SRR25508750"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508751/SRR25508751"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508752/SRR25508752"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508753/SRR25508753"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508754/SRR25508754"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508755/SRR25508755"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR025/25508/SRR25508756/SRR25508756.lite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508757/SRR25508757"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508758/SRR25508758"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508759/SRR25508759"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508760/SRR25508760"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508761/SRR25508761"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508762/SRR25508762"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508763/SRR25508763"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR025/25508/SRR25508764/SRR25508764.lite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508765/SRR25508765"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508766/SRR25508766"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508767/SRR25508767"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508768/SRR25508768"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508769/SRR25508769"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508770/SRR25508770"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508771/SRR25508771"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508772/SRR25508772"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR025/25508/SRR25508773/SRR25508773.lite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508774/SRR25508774"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508775/SRR25508775"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508776/SRR25508776"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508730/SRR25508730"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508729/SRR25508729"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508728/SRR25508728"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508727/SRR25508727"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508726/SRR25508726"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508725/SRR25508725"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508776/SRR25508776"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508775/SRR25508775"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508774/SRR25508774"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508772/SRR25508772"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508771/SRR25508771"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508770/SRR25508770"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508769/SRR25508769"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508768/SRR25508768"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508767/SRR25508767"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508766/SRR25508766"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508765/SRR25508765"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508763/SRR25508763"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508759/SRR25508759"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508760/SRR25508760"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508761/SRR25508761"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508762/SRR25508762"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508758/SRR25508758"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508757/SRR25508757"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508755/SRR25508755"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508754/SRR25508754"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508753/SRR25508753"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508752/SRR25508752"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508749/SRR25508749"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508750/SRR25508750"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508751/SRR25508751"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508747/SRR25508747"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508748/SRR25508748"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508745/SRR25508745"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508746/SRR25508746"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508743/SRR25508743"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508744/SRR25508744"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508741/SRR25508741"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508742/SRR25508742"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508739/SRR25508739"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508740/SRR25508740"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508737/SRR25508737"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508738/SRR25508738"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508735/SRR25508735"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508736/SRR25508736"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508733/SRR25508733"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508734/SRR25508734"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508731/SRR25508731"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25508732/SRR25508732"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR025/25508/SRR25508756/SRR25508756.lite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR025/25508/SRR25508764/SRR25508764.lite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR025/25508/SRR25508773/SRR25508773.lite.1"

echo "Download complete. Files saved to $OUTDIR"