Question: Cuffmerge ValueError merging assembled transcripts
gravatar for mk14609
22 months ago by
mk146090 wrote:

I am attempting to analyse my first RNA-seq experiment using Tuxedo tools. When I attempt to cuffmerge my assembled transcripts from cufflinks I get an error "Fatal error: Matched on Error Error running cuffmerge." and looking at the issue it says: "ValueError: invalid literal for int() with base 10: " I have attempted using older versions of cuffmerge 0.0.6 and rerunning cufflinks. I am pretty stuck with little experience on the platform. Any help would be much appreciated.

rna-seq cufflinks galaxy • 571 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by mk146090
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I see the bug report you sent in about the same problem.

This error occurs when the Custom reference genome is malformed or when there is a reference genome mixup. All inputs and database assignments must be from the exact same genome build.

Here is how to double check your inputs:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson25k
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