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Old 07-04-2014, 11:01 AM   #3
thickrick99
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Location: Washington

Join Date: Jul 2014
Posts: 21
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Thanks blancha for your advice especially on the FPKM values! Yeah it makes sense to keep them since I can identify genes that are not expressed.

Sorry for the really broad questions. Essentially I just needed some advice on what to do next.

One question which I believe I mentioned above was using cufflinks with and without the reference. How can I view the novel transcripts that cufflinks found without the reference in de novo mode compared to the output file using the reference?

Lastly, does anyone know a good way to identify SNV's from the data? I wasn't sure how to approach this either. Thanks!
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