Re: [galaxy-user] customizing mm9 mouse reference genome and then using that as the ref genome when uploading Illumina data

2011-10-13 Thread Jennifer Jackson
Hi Christopher, The target reference genome can be any fasta file in your history, for most tools, including mapping tools. However, the assigned database attribute for any datasets that you want to map to this custom reference would be left as undefined in Galaxy (but this would have no

Re: [galaxy-user] Problem with Cuffcompare

2011-10-13 Thread Chandu Galaxy
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.eduwrote: Chandu, There are two problems: (1) you mapped your reads to AgamP3, but the dbkeys for all of your Cufflinks datasets is anoGam1. This

Re: [galaxy-user] Problem with new tool shed

2011-10-13 Thread Greg Von Kuster
Hello Forent, On Oct 13, 2011, at 2:48 AM, Florent Angly wrote: But maybe I need a little bit of guidance with this because the example shown, the user is given a _limited_ number of output datasets to choose from. The Grinder case seems simple: give the user a field where he can

Re: [galaxy-user] Problem with Cuffcompare

2011-10-13 Thread Jeremy Goecks
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?