4.2 Raw data download¶

Purpose¶

Download public RNA-seq and Ribo-seq datasets or organize user-provided FASTQ files.

Input¶

Input	Description
SRA accession	SRR/SRX/SRP/GSE identifiers
output directory	raw data storage directory
SRA Toolkit	`prefetch`, `fastq-dump` or `fasterq-dump`
compression tool	`pigz` or `gzip`

RNA-seq raw data example¶

mkdir -p ./sce/2.rawdata/rna-seq/
cd ./sce/2.rawdata/rna-seq/

for sra in SRR1944925 SRR1944926 SRR1944927 SRR1944928 SRR1944929 SRR1944930 \
           SRR1944931 SRR1944932 SRR1944933 SRR1944934 SRR1944935
do
  prefetch -o ${sra}.sra ${sra}
  fastq-dump ${sra}.sra
  pigz ${sra}.fastq
done

Ribo-seq raw data example¶

mkdir -p ./sce/2.rawdata/ribo-seq/
cd ./sce/2.rawdata/ribo-seq/

for sra in SRR1944912 SRR1944913 SRR1944914 SRR1944915 SRR1944916 SRR1944917 \
           SRR1944918 SRR1944919 SRR1944920 SRR1944921 SRR1944922 SRR1944923
do
  prefetch -o ${sra}.sra ${sra}
  fastq-dump ${sra}.sra
  pigz ${sra}.fastq
done

Output¶

File	Description
`*.sra`	downloaded SRA archive
`*.fastq.gz`	compressed FASTQ file