Chandu, I've deleted my copy of your history to save space as your history was quite large. Please rerun Cuffcompare with the modifications I suggested below. Thanks, J. On Oct 13, 2011, at 4:26 PM, Chandu Galaxy wrote:
Thank you very much Jeremy.
Can I have a look at the re-ran datasets?
On Thu, Oct 13, 2011 at 12:12 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote: Chandu,
There are two problems:
(1) you mapped your reads to AgamP3, but the dbkeys for all of your Cufflinks datasets is anoGam1. This should not have happened automatically with Galaxy, but I'm looking into the issue now. Did you do this yourself?
(2) Galaxy does not have sequence data for anoGam1, and this directly led to the problem that you're seeing.
I corrected the problem by manually assigning build AgamP3 to your Cufflinks datasets and then rerunning Cuffcompare. In the future, I expect that we'll add anoGam1 data to our public server, but it's not clear when this will occur.
Thanks, J.
On Oct 12, 2011, at 5:35 PM, Chandu Galaxy wrote:
Thank you Jeremy. I've shared my History named 'Mosquito Work: RNA-Seq analysis 2' with you just now. Please see the datasets from 1-58 (also see deleted datasets). Thanks.
-- Chandu
On Wed, Oct 12, 2011 at 2:02 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote: Chandu,
Are you running your analysis on our public server ( main.g2.bx.psu.edu )? If so, can you share your history me please (Options-->Share/Publish-->Share with a User-->my email address).
Thanks, J.
On Oct 11, 2011, at 4:26 PM, Chandu Galaxy wrote:
Thank you for the response. I can't check my reference genome dataset because I'm using reference provided by Galaxy (Mosquito (Anopheles gambiae): AgamP3). Is there any solution? Thank you.
-- Chandu
On Mon, Oct 10, 2011 at 7:15 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Tool execution generated the following error message: Error running cuffcompare. Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu). No fasta index found for ./input1. Rebuilding, please wait.. Error: sequence lines in a FASTA record must have the same length! Chandu,
Cufflinks/compare/diff requires that your reference genome dataset have the following format:
my_chrom AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT ...
Note that all lines of sequence data have the same length.
The problem you're seeing is because there are lines in your sequence data that are not the same length, e.g.
my_chrom AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTA AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCG ...
The FASTA Width tool in Galaxy can help you format your dataset correctly.
Good luck, J.