#!/usr/bin/env bash # Bulk download script for GSE133509 # Generated from Yeo Lab Publications Database # Total files: 29 OUTDIR="GSE133509" mkdir -p "$OUTDIR" cd "$OUTDIR" # --- GEO supplementary files --- wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE133nnn/GSE133509/suppl/GSE133509_RAW.tar" -O "GSE133509_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 "${stem}.fq.gz" return 0 fi return 1 } # Option A: Download via SRA Toolkit (recommended) fasterq-dump --split-files "SRR9611927" gz1="$(_compress_if_exists 'SRR9611927_1' || true)" gz2="$(_compress_if_exists 'SRR9611927_2' || true)" gzs="$(_compress_if_exists 'SRR9611927' || true)" fasterq-dump --split-files "SRR9611928" gz1="$(_compress_if_exists 'SRR9611928_1' || true)" gz2="$(_compress_if_exists 'SRR9611928_2' || true)" gzs="$(_compress_if_exists 'SRR9611928' || true)" fasterq-dump --split-files "SRR9611929" gz1="$(_compress_if_exists 'SRR9611929_1' || true)" gz2="$(_compress_if_exists 'SRR9611929_2' || true)" gzs="$(_compress_if_exists 'SRR9611929' || true)" fasterq-dump --split-files "SRR9611930" gz1="$(_compress_if_exists 'SRR9611930_1' || true)" gz2="$(_compress_if_exists 'SRR9611930_2' || true)" gzs="$(_compress_if_exists 'SRR9611930' || true)" fasterq-dump --split-files "SRR9611931" gz1="$(_compress_if_exists 'SRR9611931_1' || true)" gz2="$(_compress_if_exists 'SRR9611931_2' || true)" gzs="$(_compress_if_exists 'SRR9611931' || true)" fasterq-dump --split-files "SRR9611932" gz1="$(_compress_if_exists 'SRR9611932_1' || true)" gz2="$(_compress_if_exists 'SRR9611932_2' || true)" gzs="$(_compress_if_exists 'SRR9611932' || true)" fasterq-dump --split-files "SRR9611933" gz1="$(_compress_if_exists 'SRR9611933_1' || true)" gz2="$(_compress_if_exists 'SRR9611933_2' || true)" gzs="$(_compress_if_exists 'SRR9611933' || true)" fasterq-dump --split-files "SRR9611934" gz1="$(_compress_if_exists 'SRR9611934_1' || true)" gz2="$(_compress_if_exists 'SRR9611934_2' || true)" gzs="$(_compress_if_exists 'SRR9611934' || true)" fasterq-dump --split-files "SRR9611935" gz1="$(_compress_if_exists 'SRR9611935_1' || true)" gz2="$(_compress_if_exists 'SRR9611935_2' || true)" gzs="$(_compress_if_exists 'SRR9611935' || true)" fasterq-dump --split-files "SRR9611936" gz1="$(_compress_if_exists 'SRR9611936_1' || true)" gz2="$(_compress_if_exists 'SRR9611936_2' || true)" gzs="$(_compress_if_exists 'SRR9611936' || true)" fasterq-dump --split-files "SRR9611937" gz1="$(_compress_if_exists 'SRR9611937_1' || true)" gz2="$(_compress_if_exists 'SRR9611937_2' || true)" gzs="$(_compress_if_exists 'SRR9611937' || true)" fasterq-dump --split-files "SRR9611938" gz1="$(_compress_if_exists 'SRR9611938_1' || true)" gz2="$(_compress_if_exists 'SRR9611938_2' || true)" gzs="$(_compress_if_exists 'SRR9611938' || true)" fasterq-dump --split-files "SRR9611939" gz1="$(_compress_if_exists 'SRR9611939_1' || true)" gz2="$(_compress_if_exists 'SRR9611939_2' || true)" gzs="$(_compress_if_exists 'SRR9611939' || true)" fasterq-dump --split-files "SRR9611940" gz1="$(_compress_if_exists 'SRR9611940_1' || true)" gz2="$(_compress_if_exists 'SRR9611940_2' || true)" gzs="$(_compress_if_exists 'SRR9611940' || true)" # Option B: Direct download (larger .sra files) curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611927/3_5_1C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611928/17_1_1T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611929/17_1_2T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611930/17_1_3T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611931/17_1_1C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611932/17_1_2C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611933/17_1_3C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611934/3_7_1C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611935/17_2_1T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611936/17_2_2T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611937/17_2_3T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611938/17_2_1C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611939/17_2_2C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611940/17_2_3C_TK_possorted_genome_bam.bam.1" # --- Additional data files --- curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611931/17_1_1C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611928/17_1_1T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611932/17_1_2C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611929/17_1_2T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611933/17_1_3C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611930/17_1_3T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611938/17_2_1C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611935/17_2_1T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611939/17_2_2C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611936/17_2_2T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611940/17_2_3C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611937/17_2_3T_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611927/3_5_1C_TK_possorted_genome_bam.bam.1" curl -L -O -C - "https://sra-pub-src-2.s3.amazonaws.com/SRR9611934/3_7_1C_TK_possorted_genome_bam.bam.1" echo "Download complete. Files saved to $OUTDIR"