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.goe...@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.goe...@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.goe...@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. >>> >> >> > >
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