Hello Irene,

On 7/21/12 5:00 AM, i b wrote:
Hello,
if I am looking for DE between samples and ran cufflinks without
reference annotation, does it mean that when I ran cuffcompare and
cuffmerge I DOTN'T HAVE to select a refence annotation in the options?

No, you do not have to use a reference annotation, but this will mean that some Cuffdiff calculations will be skipped. This is related to the reply I just sent to your other question about absent calculations.
More detail:
http://cufflinks.cbcb.umd.edu/tutorial.html#differential
http://cufflinks.cbcb.umd.edu/howitworks.html#hdif


Also,how are my cufflinks fected wheter i use the reference annotation
or not?In galaxy tracker, looks like there are alignments missing or
added compared to when i ran cufflinks with a reference annotation

Reference annotation transcripts can become part of the overall transcript dataset.
More detail:
http://cufflinks.cbcb.umd.edu/howitworks.html#hrga


Sorry to point you back to the tool documentation, but that is the resource for these topics.

Full resources are outlined in this wiki link, including the tool author's publication that Jeremy recommended:
http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results
(see "Tools on the Main server -> Example: unexpected results with RNA-seq analysis tools.)

Best,

Jen
Galaxy team


Thanks,
ib
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Jennifer Jackson
http://galaxyproject.org
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