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Question: CuffMerge Fails to accept hg19 human Sequence Data
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gravatar for rjames
12 months ago by
rjames • 0
rjames • 0 wrote:

TopHat 2.1.1 and Cufflinks appear to work properly. After the tool cufflinks, the next tool in my pipeline is Cuffmerge.

In running Cuffmerge, I use the reference for human genome: hg19.fasta. I downloaded the GRCh37/hg19 full data set as a twoBit file from http://hgdownload.soe.ucsc.edu/downloads.html#human then I used the tool twoBitToFa to convert the twobit file into a fasta file (hg19.fasta).

“Use Sequence Data” answer: Yes “Choose the source for the reference list” answer: History “Using reference file” answer: hg19.fasta (from above)

When I execute, I get a red highlight saying: “the selected case is unavailable/invalid” and Galaxy stops.

Any ideas on the cause of this?
reference sequence cufflinks cuffmerge • 335 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by rjames • 0
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I haven't seen this error before but it might be related your fasta file content. This is how to format a custom reference genome: https://galaxyproject.org/learn/custom-genomes/

It would be best to use the same reference genome that was used with Tophat for alignment with the downstream tool Cuffmerge. It can be a natively indexed genome or one in fasta format from the history. This also helps avoid other problems that can come up with chromosome/build mismatch problems.

Support FAQs: https://galaxyproject.org/support/

Hope that helps, Jen, Galaxy team
ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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