[galaxy-user] Importing GTF into Galaxy

2011-02-17 Thread Martin, David A.
Hi, I have been trying to get reference data from the ucsc browser into Galaxy, but when I try to get the rat genome in gtf format, I only get files halfway through chomosome 10. This happens with both of the available builds for the rat. I am guessing this is a problem with the UCSC files a

[galaxy-user] Using the public server for analysis

2011-01-31 Thread Martin, David A.
Rory Kirchner Cc: Martin, David A.; galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] Galaxy for gene expression comparison > > > I have patched galaxy to have cuffdiff handle replicates and to do > normalization, when that gets merged into the main branch your workflow will > be

Re: [galaxy-user] Galaxy for gene expression comparison

2011-01-20 Thread Martin, David A.
Sent: Tue 1/18/2011 9:29 PM To: Martin, David A. Cc: eaf...@emory.edu; galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] Galaxy for gene expression comparison > I am comparing RNA expression in two groups of rats, a drug treated group > against a control group. There are 10 biological re

[galaxy-user] Galaxy for gene expression comparison

2011-01-18 Thread Martin, David A.
Hello, I am comparing RNA expression in two groups of rats, a drug treated group against a control group. There are 10 biological replicates in each group. I am unsure of how to flow this analysis through Galaxy using Tophat followed by Cufflinks/compare/diff. Should the files for each group