cuffdiff with heterogeneous library types

[Wallysb01]

I want to run cuffdiff on a set of samples were some are standard illumina library and other are the dUTP library type. It does not appear that I can specify this library type for each sample.

I was wondering, has anyone ran into this before? Any advice from the seqanswers crowd?

[vivienne_lovely]

I want to run cuffdiff on a set of samples were some are standard illumina library and other are the dUTP library type. It does not appear that I can specify this library type for each sample.

I was wondering, has anyone ran into this before? Any advice from the seqanswers crowd?

Hi,everyone,
I have the same question.Could any one do me the favor? Thanks!

[agwe]

I have the same problem - data from my original experiment was unstranded, later one of the samples was resequenced due to bad quality in first run. Unfortunately, the new sample was sequenced with a stranded library.

Did you manage to figure out how to analyze different library-types samples together using Cufflinks/Cuffdiff?