18 Jan
2011
18 Jan
'11
1:35 a.m.
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 be merged at any point? I would think they should be kept separate in order to properly account for the spread across animals. I am just a little unsure of how to group the files on galaxy, and where to differentiate biological and technical replicates. On a different note, is there a way to control the bowtie mapping parameters more closely when using tophat? Thank you for any kind of knowledge on these matters! -David Martin