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  • Wallysb01
    Senior Member
    • Feb 2011
    • 286
    #1

    cuffdiff with heterogeneous library types

    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?
    Tags: None
    • vivienne_lovely
      Member
      • Oct 2011
      • 20
      #2
      Originally posted by Wallysb01 View Post
      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!

        Comment

        • agwe
          Junior Member
          • Oct 2010
          • 6
          #3
          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?

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