Question: How to use cuffmerge and cuffdiff
gravatar for lrm_1985
19 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 • 2.2k views
ADD COMMENTlink modified 13 months ago by h.jagatia0 • written 19 months ago by lrm_19850
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k 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 19 months ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 19 months ago by lrm_19850
gravatar for h.jagatia
13 months ago by
h.jagatia0 wrote:

Hi, So I have run Cuffmerge, Cuffquant and Cuffdiff, which gives me one value for 3 biological replicates of each strain that I wish to compare. However one biological replicate can be the difference between a significant log2 fold change, therefore why would you merge the biological replicates?

ADD COMMENTlink written 13 months ago by h.jagatia0

Keep biological replicates distinct to compare those conditions. Technical replicates are different - sometimes useful to merge (final analysis) but sometimes useful to leave distinct (for QA purposes).

The current tutorials linked above have examples of both.

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson25k
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