Question: Illumina Platinum Genomes md5 checksums
0
gravatar for sboardman
4.0 years ago by
sboardman0
United Kingdom
sboardman0 wrote:

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

checksum ebi • 1.6k views
ADD COMMENTlink modified 4.0 years ago by Saulius Lukauskas530 • written 4.0 years ago by sboardman0
2
gravatar for Saulius Lukauskas
4.0 years ago by
London, UK
Saulius Lukauskas530 wrote:

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

ADD COMMENTlink written 4.0 years ago by Saulius Lukauskas530

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.

ADD REPLYlink written 4.0 years ago by sboardman0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1879 users visited in the last hour