Hello Irene,
Please see below:
On 7/23/12 2:17 AM, i b wrote:
Thanks Jen.
One thing I still don't get: what if I want to discover novel
tanscripts? Does this have anythign to do with selecting or not a
reference annotation
Best
I
On Mon, Jul 23, 2012 at 5:58 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
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
On this page, the sections titled "Discovering novel genes and
transcripts" and "Differential analysis with gene and transcript
discovery" cover when to use a reference annotation file during the
various stages of analysis for different end purposes. The publication
also includes more details.
Going forward, please be sure to send questions directly to the mailing
list, as this helps us to both track and coordinate replies as a team.
Thanks,
Jen
Galaxy team
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
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
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