Ronald Robertson

Sanjay Singh

Scientist/Writer
  • Emailsanjaysingh765@gmail.com
  • Socail@lampatlex
  • VisitorSince 1982
  • LocationKentucky, USA



Easiest Way to Download All Sra Samples or Multi Experiment file from NCBI SRA database



European Nucleotide Archive is good place to start to download the raw fastq files. But it is not easy to download multiple run files from NCBI SRA database. I recently learn to download in relatively easy way. I want to download these four run together from NCBI SRA database : SRR122247,SRR122248,SRR122249, SRR122250. Format of basic url is like that


ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/{SRR|ERR|DRR}/<first 6 characters of accession>/<accession>/<accession>.sra


Where

{SRR|ERR|DRR} should be either ‘SRR’, ‘ERR’, or ‘DRR’ and should match the prefix of the target .sra file


Described in details HERE.
So my final urls will look like this



ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR122/SRR122247/SRR122247.sra
ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR122/SRR122248/SRR122248.sra
ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR122/SRR122249/SRR122249.sra
ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR122/SRR122250/SRR122250.sra



Now save this urls in a text file (url_list.txt, for example). Run the wget like this

wget -i url_list.txt


run sudo apt-get install wget from terminal if you don't have wget






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