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Old 05-07-2012, 01:11 PM   #1
Wallysb01
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Default 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?
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Old 07-02-2013, 07:36 PM   #2
vivienne_lovely
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Quote:
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!
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Old 04-07-2014, 02:16 PM   #3
agwe
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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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