Question: CuffMerge Fails to accept hg19 human Sequence Data
gravatar for rjames
12 months ago by
rjames0 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 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?

ADD COMMENTlink modified 12 months ago by Jennifer Hillman Jackson25k • written 12 months ago by rjames0
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

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:

Hope that helps, Jen, Galaxy team

ADD COMMENTlink written 12 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: 169 users visited in the last hour