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Question: Cufflinks Eference Annotation
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gravatar for i b
6.4 years ago by
i b • 330
i b • 330 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? 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 Thanks, ib
rna-seq cuffmerge cufflinks • 1.1k views
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modified 6.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.4 years ago by i b • 330
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gravatar for Jennifer Hillman Jackson
6.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Irene, 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 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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.4 years ago by Jennifer Hillman Jackson ♦ 25k
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