MD5Sums of fastq files from SRA

Question

[ildem]

Hi all,

I downloaded a bunch of fastq files using wget. i.e. wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/072/SRR13198172/SRR13198172.fastq.gz

I did this because SRA download was either failing or taking forever.

I need to verify file integrity with MD5sums. Is there a way to get this information? or extract it from SRA somehow?

thanks!

Answer 1

[ATpoint]

Tbh I would just download it via the Aspera links. Aspera is smart and only creates the final file if the download finishes successfully, so md5 are not necessary here.

Answer 2

[dariober]

Query ENA archive and select sra_md5 as one of the output fields (I think that's what you want). In practice, though, I think that checking the integrity of the gzip file (gzip -t) should give you a pretty good reassurance that the file is complete.