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
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