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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):
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#!/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 varaiblesSRA identifiers SRAID=SRR1002659 ### Pipeline #Step1: Download SRA file prefetch ${SRAID} #Step2: Extract FASTQ file(s) from SRA file fastq-dump --split-files ${SRAID} |
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