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Question: Problem with using CuffMerge in Galaxy
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gravatar for nazaninhoseinkhan
2.5 years ago by
nazaninhoseinkhan • 10
nazaninhoseinkhan • 10 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

Nazanin
rna-seq cuffmerge galaxy importing gtf • 761 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by nazaninhoseinkhan • 10

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

ADD REPLY • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi Nazanin,

I am unable to reproduce the Cuffmerge tool form behavior at http://usegalaxy.org.

Perhaps there is a datatype assignment problem, in which case this should help: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

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: https://wiki.galaxyproject.org/PublicGalaxyServers

Best, Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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