Question: Cummerbund visualization of expression plot
gravatar for clarkd
4 months ago by
clarkd30 wrote:

I am following the NGS101-16 video on Cuffdiff/Cummerbund to learn how to use Cummerbund. For expression plot, Cummerbund is unable to detect Gene ID and registers a value of "null". If I go ahead and execute, it reports the error "Parameter gene_id requires a value, but has no legal values defined". I am able to generate a SQLlite database and Cummerbund detects that file. It can make other visualizations of the data that don't require gene_id to be entered.

rna-seq • 264 views
ADD COMMENTlink modified 9 weeks ago by roxy.zhang0 • written 4 months ago by clarkd30

Deprecated reply - has since been confirmed as an issue. See other comments for a link to the ticket.


For this tutorial, the two prior videos show the prep steps. Did you follow these protocols as well? With all the jobs run in Galaxy?

Whether using your own data or the tutorial data, make sure that reference annotation is used (GTF) and that it is associated with the same exact reference genome as used for mapping. Specifically, double check that the build is the same and that the chromosome identifiers are exactly the same.

You can double check for this value being present in your data at different steps - check the GTF dataset attributes first to confirm this value (gene_id) is included then check after Cufflinks, or after Cuffdiff, or even by extracting tables from the SQLite database (that contain the value).

Also, the expression plot in the video is for the level "isoforms". For the same/similar results as in the tutorial, use the same options.

If you are working at or can reproduce the issue there - after reviewing and confirming the above - a bug report from an error dataset can be sent in. Please leave all inputs undeleted in the history. This is how:

Thanks, Jen, Galaxy team

ADD REPLYlink modified 11 weeks ago • written 4 months ago by Jennifer Hillman Jackson22k

Did you ever get it to work? I'm having the same problems in cummeRbund. Gene_ID null. I'm debating going through that whole tutorial just to see if I could get it to work once, but I don't want to waste my time if it isn't going to work.

ADD REPLYlink written 12 weeks ago by hershbc30

No, I didn't! I seemed to be doing all the right things but I ran out of time.

ADD REPLYlink written 12 weeks ago by clarkd30

Looks like they are trying to solve it!

ADD REPLYlink written 11 weeks ago by hershbc30
gravatar for roxy.zhang
9 weeks ago by
roxy.zhang0 wrote:


I am having the exact same problem here! I seem to have done everything right but the gene_id part just keep sowing up as null for some reason. Did you guys every get it solved? Thanks a lot!

ADD COMMENTlink written 9 weeks ago by roxy.zhang0
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