#!/usr/bin/env bash # Bulk download script for GSE34995 # Generated from Yeo Lab Publications Database # Total files: 68 OUTDIR="GSE34995" mkdir -p "$OUTDIR" cd "$OUTDIR" # --- GEO supplementary files --- wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34995/suppl/GSE34995_RAW.tar" -O "GSE34995_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 "${stem}.fq.gz" return 0 fi return 1 } # Option A: Download via SRA Toolkit (recommended) fasterq-dump --split-files "SRR398210" gz1="$(_compress_if_exists 'SRR398210_1' || true)" gz2="$(_compress_if_exists 'SRR398210_2' || true)" gzs="$(_compress_if_exists 'SRR398210' || true)" fasterq-dump --split-files "SRR398211" gz1="$(_compress_if_exists 'SRR398211_1' || true)" gz2="$(_compress_if_exists 'SRR398211_2' || true)" gzs="$(_compress_if_exists 'SRR398211' || true)" fasterq-dump --split-files "SRR398212" gz1="$(_compress_if_exists 'SRR398212_1' || true)" gz2="$(_compress_if_exists 'SRR398212_2' || true)" gzs="$(_compress_if_exists 'SRR398212' || true)" fasterq-dump --split-files "SRR398213" gz1="$(_compress_if_exists 'SRR398213_1' || true)" gz2="$(_compress_if_exists 'SRR398213_2' || true)" gzs="$(_compress_if_exists 'SRR398213' || true)" fasterq-dump --split-files "SRR398214" gz1="$(_compress_if_exists 'SRR398214_1' || true)" gz2="$(_compress_if_exists 'SRR398214_2' || true)" gzs="$(_compress_if_exists 'SRR398214' || true)" fasterq-dump --split-files "SRR398215" gz1="$(_compress_if_exists 'SRR398215_1' || true)" gz2="$(_compress_if_exists 'SRR398215_2' || true)" gzs="$(_compress_if_exists 'SRR398215' || true)" fasterq-dump --split-files "SRR398216" gz1="$(_compress_if_exists 'SRR398216_1' || true)" gz2="$(_compress_if_exists 'SRR398216_2' || true)" gzs="$(_compress_if_exists 'SRR398216' || true)" fasterq-dump --split-files "SRR398217" gz1="$(_compress_if_exists 'SRR398217_1' || true)" gz2="$(_compress_if_exists 'SRR398217_2' || true)" gzs="$(_compress_if_exists 'SRR398217' || true)" fasterq-dump --split-files "SRR398218" gz1="$(_compress_if_exists 'SRR398218_1' || true)" gz2="$(_compress_if_exists 'SRR398218_2' || true)" gzs="$(_compress_if_exists 'SRR398218' || true)" fasterq-dump --split-files "SRR398219" gz1="$(_compress_if_exists 'SRR398219_1' || true)" gz2="$(_compress_if_exists 'SRR398219_2' || true)" gzs="$(_compress_if_exists 'SRR398219' || true)" fasterq-dump --split-files "SRR398220" gz1="$(_compress_if_exists 'SRR398220_1' || true)" gz2="$(_compress_if_exists 'SRR398220_2' || true)" gzs="$(_compress_if_exists 'SRR398220' || true)" fasterq-dump --split-files "SRR398221" gz1="$(_compress_if_exists 'SRR398221_1' || true)" gz2="$(_compress_if_exists 'SRR398221_2' || true)" gzs="$(_compress_if_exists 'SRR398221' || true)" fasterq-dump --split-files "SRR398222" gz1="$(_compress_if_exists 'SRR398222_1' || true)" gz2="$(_compress_if_exists 'SRR398222_2' || true)" gzs="$(_compress_if_exists 'SRR398222' || true)" fasterq-dump --split-files "SRR398223" gz1="$(_compress_if_exists 'SRR398223_1' || true)" gz2="$(_compress_if_exists 'SRR398223_2' || true)" gzs="$(_compress_if_exists 'SRR398223' || true)" fasterq-dump --split-files "SRR398224" gz1="$(_compress_if_exists 'SRR398224_1' || true)" gz2="$(_compress_if_exists 'SRR398224_2' || true)" gzs="$(_compress_if_exists 'SRR398224' || true)" fasterq-dump --split-files "SRR398225" gz1="$(_compress_if_exists 'SRR398225_1' || true)" gz2="$(_compress_if_exists 'SRR398225_2' || true)" gzs="$(_compress_if_exists 'SRR398225' || true)" fasterq-dump --split-files "SRR398226" gz1="$(_compress_if_exists 'SRR398226_1' || true)" gz2="$(_compress_if_exists 'SRR398226_2' || true)" gzs="$(_compress_if_exists 'SRR398226' || true)" fasterq-dump --split-files "SRR398227" gz1="$(_compress_if_exists 'SRR398227_1' || true)" gz2="$(_compress_if_exists 'SRR398227_2' || true)" gzs="$(_compress_if_exists 'SRR398227' || true)" fasterq-dump --split-files "SRR398228" gz1="$(_compress_if_exists 'SRR398228_1' || true)" gz2="$(_compress_if_exists 'SRR398228_2' || true)" gzs="$(_compress_if_exists 'SRR398228' || true)" fasterq-dump --split-files "SRR398229" gz1="$(_compress_if_exists 'SRR398229_1' || true)" gz2="$(_compress_if_exists 'SRR398229_2' || true)" gzs="$(_compress_if_exists 'SRR398229' || true)" fasterq-dump --split-files "SRR398230" gz1="$(_compress_if_exists 'SRR398230_1' || true)" gz2="$(_compress_if_exists 'SRR398230_2' || true)" gzs="$(_compress_if_exists 'SRR398230' || true)" fasterq-dump --split-files "SRR398231" gz1="$(_compress_if_exists 'SRR398231_1' || true)" gz2="$(_compress_if_exists 'SRR398231_2' || true)" gzs="$(_compress_if_exists 'SRR398231' || true)" fasterq-dump --split-files "SRR398232" gz1="$(_compress_if_exists 'SRR398232_1' || true)" gz2="$(_compress_if_exists 'SRR398232_2' || true)" gzs="$(_compress_if_exists 'SRR398232' || true)" fasterq-dump --split-files "SRR398233" gz1="$(_compress_if_exists 'SRR398233_1' || true)" gz2="$(_compress_if_exists 'SRR398233_2' || true)" gzs="$(_compress_if_exists 'SRR398233' || true)" fasterq-dump --split-files "SRR398234" gz1="$(_compress_if_exists 'SRR398234_1' || true)" gz2="$(_compress_if_exists 'SRR398234_2' || true)" gzs="$(_compress_if_exists 'SRR398234' || true)" fasterq-dump --split-files "SRR398235" gz1="$(_compress_if_exists 'SRR398235_1' || true)" gz2="$(_compress_if_exists 'SRR398235_2' || true)" gzs="$(_compress_if_exists 'SRR398235' || true)" fasterq-dump --split-files "SRR398236" gz1="$(_compress_if_exists 'SRR398236_1' || true)" gz2="$(_compress_if_exists 'SRR398236_2' || true)" gzs="$(_compress_if_exists 'SRR398236' || true)" fasterq-dump --split-files "SRR398237" gz1="$(_compress_if_exists 'SRR398237_1' || true)" gz2="$(_compress_if_exists 'SRR398237_2' || true)" gzs="$(_compress_if_exists 'SRR398237' || true)" fasterq-dump --split-files "SRR398238" gz1="$(_compress_if_exists 'SRR398238_1' || true)" gz2="$(_compress_if_exists 'SRR398238_2' || true)" gzs="$(_compress_if_exists 'SRR398238' || true)" fasterq-dump --split-files "SRR398239" gz1="$(_compress_if_exists 'SRR398239_1' || true)" gz2="$(_compress_if_exists 'SRR398239_2' || true)" gzs="$(_compress_if_exists 'SRR398239' || true)" fasterq-dump --split-files "SRR398240" gz1="$(_compress_if_exists 'SRR398240_1' || true)" gz2="$(_compress_if_exists 'SRR398240_2' || true)" gzs="$(_compress_if_exists 'SRR398240' || true)" # Option B: Direct download (larger .sra files) curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398210/SRR398210" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398211/SRR398211" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398212/SRR398212" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398213/SRR398213" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398214/SRR398214" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398215/SRR398215" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398216/SRR398216" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398217/SRR398217" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398218/SRR398218" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398219/SRR398219" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398220/SRR398220" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398221/SRR398221" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398222/SRR398222" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398223/SRR398223" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398224/SRR398224" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398225/SRR398225" curl -L -O -C - "https://sra-pub-src-1.s3.amazonaws.com/SRR398226/hnRNPM_293T_RNAseq_KD1b_sequence.txt.1" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398227/SRR398227" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398228/SRR398228" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398229/SRR398229" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398230/SRR398230" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398231/SRR398231" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398232/SRR398232" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398233/SRR398233" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398234/SRR398234" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398235/SRR398235" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398236/SRR398236" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398237/SRR398237" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398238/SRR398238" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398239/SRR398239" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398240/SRR398240" # --- Additional data files --- curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398235/SRR398235" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398236/SRR398236" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398237/SRR398237" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR000/398/SRR398238.sralite.1" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398238/SRR398238" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398239/SRR398239" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398240/SRR398240" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398210/SRR398210" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398211/SRR398211" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398212/SRR398212" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398213/SRR398213" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398214/SRR398214" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398215/SRR398215" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398216/SRR398216" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398217/SRR398217" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398218/SRR398218" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398219/SRR398219" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398220/SRR398220" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398221/SRR398221" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398222/SRR398222" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398223/SRR398223" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398224/SRR398224" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398225/SRR398225" curl -L -O -C - "https://sra-pub-src-1.s3.amazonaws.com/SRR398226/hnRNPM_293T_RNAseq_KD1b_sequence.txt.1" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398227/SRR398227" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398228/SRR398228" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398229/SRR398229" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398230/SRR398230" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398231/SRR398231" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398232/SRR398232" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398233/SRR398233" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398234/SRR398234" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398215/SRR398215" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398224/SRR398224" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398230/SRR398230" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398234/SRR398234" echo "Download complete. Files saved to $OUTDIR"