4.2 Raw data download¶

Purpose¶

Download public RNA-seq and Ribo-seq datasets, or organize user-provided FASTQ files, into the 2.rawdata directory for downstream cleaning.

The workflow is divided into three steps:

Step 1: Prepare the raw data directory
Step 2: Download RNA-seq raw data
Step 3: Download Ribo-seq raw data

All commands are run inside the 2.rawdata directory created in Step 1.

Input¶

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

Step 1: Prepare the raw data directory¶

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

Step 2: Download RNA-seq raw data¶

The following example downloads the RNA-seq samples of the public dataset used in this tutorial.

cd ./rna-seq/

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

Step 3: Download Ribo-seq raw data¶

cd ./ribo-seq/

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

Notes¶

fasterq-dump is the recommended replacement for the deprecated fastq-dump.
For paired-end data, fasterq-dump produces *.fastq files with _1/_2 suffixes; adjust the compression loop accordingly.
If you already have user-provided FASTQ files, copy them directly into 2.rawdata/rna-seq/ or 2.rawdata/ribo-seq/ and skip the download steps.
The example accessions are taken from a public dataset; replace them with the accessions of your own project.

Output¶

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