I am trying use Galaxy to analysis the yeast RNA-seq data. When I want to try the cuffmerge and cuffdiff, I have questions. For the cuffmerge, should I merge the repeat of the samples or different genotype strain? Base on this questions, how should I do when I run the the cuffdiff using the results from cuffmerge?
In short, use Cuffmerge to create a "master" GTF dataset, with the input as the result GTF datasets from Cufflinks (all produced in the experiment) plus the reference annotation GTF dataset (if one is to be used).
The result from Cuffmerge is the reference annotation GTF input to Cuffdiff. The other inputs will be the mapped BAM datasets, with replicates (1 or more) grouped by condition.
Manual and tutorial examples:
Thanks! Jen, Galaxy team