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Old 09-17-2017, 07:21 PM   #2
neavemj
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Location: MA, USA

Join Date: Feb 2014
Posts: 57
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Hi Enriquez,

You should not need to sort the bam file, so I don't think that's the problem.

Do you know if your gff file contains the 'gene_id' attribute? You can open the file in a text editor and check that this is listed. Otherwise, you can change the gene id variable using '--idattr'. This option should also be available in galaxy.

I think converting your file from gff3 to gtf is also a pretty good idea. I think I've done this in the past and it worked. The error you are getting suggests that the python library 'scipy' is not installed in your galaxy configuration. Perhaps you can get the system administrators to install it for you?

Best,

Matt.
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