Question: How to use cuffmerge and cuffdiff
gravatar for lrm_1985
6 months ago by
lrm_19850 wrote:

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?

rna-seq • 333 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson23k • written 6 months ago by lrm_19850
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson23k wrote:


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

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson23k

Thanks, I will read the examples. Hope I can figure out soon

ADD REPLYlink written 6 months ago by lrm_19850
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