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Question: Cufflinks Tool Error - mismatched chromosome identifiers in custom genome versus annotation
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gravatar for anjaligupta
6 months ago by
anjaligupta • 0
anjaligupta • 0 wrote:

Hi,

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

Thank You.
annotation custom-genome cufflinks galaxy mismatch • 177 views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by anjaligupta • 0

Troubleshooting help is here FAQs: https://galaxyproject.org/support/#troubleshooting

Start with: My job ended with an error. What can I do? https://galaxyproject.org/support/tool-error/

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

Thanks, Jen, Galaxy team

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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:

NC_008463

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:

>NC_008463

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 COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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