Question: Cufflinks Tool Error - mismatched chromosome identifiers in custom genome versus annotation
gravatar for anjaligupta
6 months ago by
anjaligupta0 wrote:


I have tried using Cufflinks for my data thrice but it is posting some error. Please let me know the underlying cause.

Thank You.

ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by anjaligupta0

Troubleshooting help is here FAQs:

Start with: My job ended with an error. What can I do?

If that doesn't help enough, what is the error message? And where are you using Galaxy?

Thanks, Jen, Galaxy team

ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I found your problematic jobs.

The root of the issue is a chromosome identifier mismatch between the custom genome used for mapping and the reference annotation GFF3 dataset.

The custom genome fasta (single sequence) has a title line in this format:

>gi|116048575|ref|NC_008463|pseudocap|138 [Pseudomonas aeruginosa UCBPP-PA14 chromosome, complete genome.]

The reference GFF3 has the chromosome identifier with this content:


Both must be an exact match when using most tools, including Cuffdiff. You'll need to edit the fasta to have this content (only) in the fasta title line:


This can be done in Galaxy (using Text Manipulation tools, as NormalizeFasta will not be enough for this data content) or edited prior to Upload to Galaxy. Once fixed, rerun the mapping jobs, then downstream tools.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour