Cole Trapnell

That would be great! Thanks for offering to help. Cole Cole Trapnell Sent from https://polymail.io/?utm_source=polymail&utm_medium=referral&utm_campaign=signature On Tue, Aug 16, 2016 at 11:28 AM jrdemasi < mailto:jrdemasi [email protected] > wrote: a,...

Are you using the precompiled binaries for Cufflinks?

So I'm no longer able to reproduce this with Bowtie 2.2.5, TopHat 2.1.0, and the current head of the develop branch. Have you tried with a recent build from source?

The new README file on the github site now includes instructions. Can you verify that you can build when following them?

I'm not sure who told you Cufflinks is a "legacy" package. We expect to add new features as the need arises, particularly in support of new single-cell applications.

Monocle doesn't support different fit types. The message there is leftover from the DESeq1 code we based our dispersion estimation procedure on. I will change the message. Regarding the issue:...

That's right - estimateDispersions only makes sense right now for negbinomial and negbinomial.size expression families. We'll add a warning for the next release that estimateDispersions has no effect for FPKM/TPM...