Question: Problem with using CuffMerge in Galaxy
gravatar for nazaninhoseinkhan
2.5 years ago by
nazaninhoseinkhan10 wrote:

Dear all,

I want to find differential expressed genes between two RNASeq samples in Galaxy.

I want to use CuffMerge to merge assembled transcripts produced by Cufflinks.

In the first box the list of all Cufflinks output is shown(when I choose multiple datasets), but when I choose the option to import additional gtf file , it is empty and says me there is nothing to show.

Can you help me find the problem

Thank you in advance


ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson25k • written 2.5 years ago by nazaninhoseinkhan10

We are testing this out - more feedback very soon. Jen, Galaxy team

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Nazanin,

I am unable to reproduce the Cuffmerge tool form behavior at

Perhaps there is a datatype assignment problem, in which case this should help:

Dataset collections versus individual datasets labeled with the metadata "dataytpe" assignment of GTF are accepted by these input fields.

If you are working on another server, then contacting the administrators is the best path forward. This list of known Public Galaxy servers (should you be working at one of these) often has contact info - or look for it on the server's home page:

Best, Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson25k
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