Illumina Platinum Genomes md5 checksums

Question

[sboardman]

Hi,

I've downloaded a set of bams from Illumina's Platinum Genomes experiment (hosted at EBI) and would like to do due diligence and perform a checksum check, but I can't find any published for these files.

Has anyone else downloaded the bam files from ftp://ftp.sra.ebi.ac.uk/vol1/ERA172/ERA172924/bam/ and run md5sum on them? These are the CEPH pedigree sequenced to 50x depth.

If so I'd be very grateful for the results to do a comparison (I can publish the checksum values I get once its finished running).

SB

Answer 1

[Saulius Lukauskas]

EBI are actually very good at storing their data and usually have the md5 checksums among the files.

To find the md5 number for your data: look at their data table for the accession number instead of raw FTP access: https://www.ebi.ac.uk/ena/data/view/ERA172924&display=html

Click on "select columns", then on "submitted md5" and voila -- md5 is there. There's a bunch of other metadata there as well.

NB: If you want to parse this from code checkout the text view.

[sboardman]

Brilliant, thanks so much for that. Been scratching my head comparing it to 1000 Genomes files which have the .bai and .bas with md5 in them.