This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to get checksums for files on BaseSpace?

A sequencing service has shared Illumina files with my BaseSpace account (I'm new to BaseSpace). I'd like to verify the integrity of these (fastq) files with those I have downloaded. How can I find the checksums for these files? (I know how to get them from my downloaded files, just not from those in BaseSpace). Also, should/can checksums be verified for the original files uploaded to BaseSpace from the sequencing center?

Thank you.

md5
• 5,401 views • link
updated by geneticatt • geneticatt • written by jbherrick • jbherrick

Have you asked Illumina/BaseSpace tech support? At least for the public data in basespace I don't see any checksums.

• 0 views • link
written by GenoMax GenoMax

I have not been able to find a tech support link on Basespace. Any idea where it might be found?

• 0 views • link
written by jbherrick • jbherrick

Start with techsupport at illumina.com.

• 0 views • link
written by GenoMax GenoMax

1 answer

bscp from the BaseSpaceCLI can download directly from BaseSpace and write the md5sums simultaneously.

bscp --write-md5 ...

Maybe some BaseSpace app will calculate md5 on the server side (or you can create an app for that, but I never created a BaseSpace app so can't help here), otherwise you will have to download the data again.

FastQC is really sensitive to data corruption, and will throw out an error or warning (e.g. for sequence and quality of different length, or for a sequence with missing quality), even if just one sequence is at fault.

• 0 views • link
written by h.mon h.mon

I am updating this thread because BaseSpaceCLI seems to have depreciated bscp. I am using bs download project --name $PROJECTID to download reads, however there is no --write-md5 flag available for this function or any other BaseSpaceCLI functions.

With BaseMount, users can navigate the BaseSpace files and run md5sum in-place, but BaseMount is no longer supported (NS2000 reads can't be accessed using BaseMount). Illumina Tech Support refers users to BaseSpace CLI for functions previously fulfilled by BaseMount. My current solution is to download the data twice and compare md5sums of the two copies. Hopefully someone knows a better way.

• 0 views • link
written by geneticatt • geneticatt

Log in to answer this question.

More posts like this