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Background and external resources

“Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data.”

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To install SRA toolkit, follow these instructions:https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit

To download data fasta files using project or biosample accession numbers:https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump

You can also use SRA Explorer to view all files in a project and download all or some of them.: https://www.biostars.org/p/385930/

Goal

Download public data deposited in NCBI’s Short Read Archive (SRA) database.

Pre-requisites (if not available)

• Installed conda3 or miniconda3 ( https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html )

• Basic unix command line knowledge (example: https://researchcomputing.princeton.edu/education/external-online-resources/linux ; https://swcarpentry.github.io/shell-novice/ )

• Familiarity with one unix text editors (example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

Installing miniconda

https://docs.conda.io/en/latest/miniconda.html#linux-installers

bash Miniconda3-latest-Linux-x86_64.sh

Install sra-tools

Once conda is installed in the instance. Go to https://anaconda.org and search for sra-tools. Copy and paste the command to install the tool in your HPC account:

conda install -c bioconda sra-tools 

Download SRA files

Example: PBS script (launch_fetch_SRAfiles.pbs) to fetch multiple files from SRA database

#!/bin/bash -l
#PBS -N SRAfiles
#PBS -l walltime=2:00:00
#PBS -l mem=4gb
#PBS -l ncpus=2
#PBS -m bae
###PBS -M email@host
#PBS -j oe

cd $PBS_O_WORKDIR

### User defined SRA identifiers
ACCESSIONS=SRR1002659,SRR1002660,SRR1002661,SRR1002662

### Pipeline

#Step1: Download SRA file
prefetch ${ACCESSIONS}

#Step2: Extract FASTQ file(s) from SRA file
fastq-dump --split-files ${ACCESSIONS}

submit PBS script to the HPC cluster

qsub launch_fetch_SRAfiles.pbs

monitor job progression

qjobs