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