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Data download using module load sra-tools
Data download using module load sra-tools
- Roberto Barrero Gumiel
Owned by Roberto Barrero Gumiel
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
SRR1039512Prepare 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 *fastqsubmit PBS script to the HPC cluster
qsub launch_fetch_SRAfiles.pbsmonitor job progression