[galaxy-user] FW: [galaxy-bugs] Galaxy tool error report from b...@leeds.ac.uk

:08 PM To: Irene Bassano Cc: galaxy-b...@bx.psu.edu Subject: Re: [galaxy-bugs] Galaxy tool error report from b...@leeds.ac.uk Hello, iGenomes covers the UCSC build, and this named Human Feb. 2009 (GRCh37/hg19) (hg19) in the full name in the UI. The hg19 key is the important part - as the name may

[galaxy-user] human genome latest annotaiton

Hi Jen, I uploaded some fastq files and selected as Genome from the drop down list Homo sapiens b37(hg_g1k_v37). Is this the same as the genome listed in UCSC February 2009 (GRCh37/hg19)? I am using iGenomes to get the gene names rather than annotation such as NM_00 and I fused the UCSC

Re: [galaxy-user] FW: Tophat/Cuff parameters

Thanks a lot Jen! Irene From: Jennifer Jackson [j...@bx.psu.edu] Sent: Saturday, November 16, 2013 6:57 PM To: Irene Bassano Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] FW: Tophat/Cuff parameters Hi, Yes, the .py part of the wrapper you

[galaxy-user] FW: Tophat/Cuff parameters

options but if some of them wont affect the final reaults then is not worth changing them. Thanks, Irene From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: 14 November 2013 21:43 To: galaxy-user Cc: Irene Bassano Subject: Tophat/Cuff parameters Hello, Yes, this is correct, not all parameters can

[galaxy-user] cufflinks reference annotation

HI guys, how do we know when to select a refernce annotation when running cufflinks?And if yes, which one from UCSC should we chose: refgene or knowngenes? Thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy

[galaxy-user] cuffdiff

Hi, just few questions about cuffdiff if anyone can answer: 1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files 2.what to use as input: cufflinks, cuffcompare or cuffmerge? Thanks a lot! ___ The Galaxy