Question: Ran the cuffdiff and showed error msg
gravatar for khksw0403
14 months ago by
khksw040310 wrote:

Hello, Galaxy staff

I have ran cuffdiff, however received error message. But, i don't know what's wrong.

(input bam file is analysis by HISAT2 and reference annotation GTF/GFF3 file is mm10 GTF file that is got from genecode homepage).


rna-seq cuffdiff • 473 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 14 months ago by khksw040310
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


First, try one rerun to eliminate a transient cluster error.

After that, without knowing the error message the root cause is difficult to guess. Below are a set of FAQs cover the most common reasons for errors. Review and then get back to us with what you checked and more details about the problem if you cannot find out how to fix the job. The issue is very likely with the inputs or tool options used if working at

Support FAQs:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k

I took a look and found the problem. The reference GTF used is based on a human genome build, not mouse. The NGS data was mapped against mouse (mm10).

The solution is to find a reference GTF dataset that is mouse but also based on the mm10 build. This prior Q&A covers common options for where to find such a file:

Mismatched genome inputs are covered in this specific FAQ:

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson25k

i do STAR aligment again and do cuffdiff analysis. so finally resolve this problem. thanks a lot.

ADD REPLYlink written 13 months ago by khksw040310
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