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Question: Cuffdiff-output-couldnot find fasta record for a scaffold
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gravatar for raj_262920
3.8 years ago by
raj_262920 • 20
Germany
raj_262920 • 20 wrote:

Dear Galaxy team

When i ran cuffdiff for my merged transcripts file using a custom reference genome, It ran successfully and i could find significant differences. But i see under the cuffdiff files, it says' couldn't find fasta record for scaffold 1 and scaffold 10, will not be considered for bias correction'.

I checked my reference genome for the respective scaffolds and they are present and i also checked the gtf file and looks like it is represented correctly. I don't know where this messages is coming from and why ?!

I think because of this it doesnt give any FPKM values for genes in those scaffolds which inturn just says NOTEST for these scaffolds. Could you please help me to possibly clear this ?

Thanks
rna-seq galaxy • 1.2k views
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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by raj_262920 • 20
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gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Double check that the chromosome identifiers are an exact match between all of the inputs. Even slight differences can be problematic. 

Also double check that data for for these chromosomes actually exists in Cuffmerge output. 

More custom reference genome troubleshooting help can be found on this wiki. Formatting can be very important. It is often necessary to do this formatting as the first step, before running any tools in the analysis (before mapping). Sometimes you can adjust a bit and it will be OK, other times not. The "Troubleshooting" section has instructions for making changes, and most can be done within Galaxy.
http://wiki.galaxyproject.org/Learn/CustomGenomes

Best, Jen, Galaxy team
ADD COMMENT • link modified 3.7 years ago • written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
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