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Data download using module load sra-tools

Data download using module load sra-tools

Owned by Roberto Barrero Gumiel
Last updated: Aug 03, 2023
1 min read

Aim:

Download FASTQ files for samples of interest.

SRA website: https://www.google.com/search?client=safari&rls=en&q=NCBI++SRA&ie=UTF-8&oe=UTF-8

Search NGS data of interest

In the ‘search box' enter one of the following identifiers:

  • Project accession (i.e., PRJNA229998)

  • Study accession (i.e., SRP033351)

  • Experiment accession (i.e., SRX384360)

  • Run accession (i.e., SRR1039508)

  • or search for keywords, for example, “RNA-seq mouse”

 

Prepare a list of SRA run accessions to be downloaded and saved in a file, for example, ‘SRR_Acc_List.txt’:

SRR1039508 SRR1039509 SRR1039510 SRR1039511 SRR1039512

Prepare a PBS Pro submission script as follows:

#!/bin/bash -l #PBS -N rna #PBS -l select=1:ncpus=1:mem=8gb #PBS -l walltime=24:00:00 #Enable the container modules source /pkg/shpc/enable #Load the SRA-TOOLS module module load sra-tools/3.0.5--h9f5acd7_1 #work on current directory (folder) cd $PBS_O_WORKDIR for i in $(cat SRR_Acc_List.txt); do echo $i prefetch.3 $i fasterq-dump.3 --split-files $i done gzip *fastq

submit PBS script to the HPC cluster

qsub launch_fetch_SRAfiles.pbs

monitor job progression

qjobs

 

 

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