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 <jen@bx.psu.edu> wrote:

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Hello Irene,

On 7/21/12 5:00 AM, i b wrote:

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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

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http://cufflinks.cbcb.umd.edu/howitworks.html#hdif

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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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Thanks, ib ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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