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09-05-2011, 12:00 PM
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#1 |
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Member
Location: il Join Date: Jun 2010
Posts: 64
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detecting alternative splicing in RNA-seq
Hello,
In RNA seq analysis - I have aligned reads to the genome and estimated the abundance of known transcripts in each sample. In the next step I would like to find genes which their "exon usage" is different between different samples. Thanks in advance for any suggestions... |
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09-05-2011, 01:37 PM
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#2 |
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Devon Ryan
Location: Freiburg, Germany Join Date: Jul 2011
Posts: 3,480
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cufflinks, specifically the cuffdiff command can do that. It would be output in the cds_exp.diff file I believe.
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09-06-2011, 12:23 AM
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#3 |
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Senior Member
Location: Paris Join Date: Aug 2011
Posts: 239
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DEXSeq too but the paper is not published yet I think
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09-06-2011, 12:24 AM
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#4 |
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Member
Location: il Join Date: Jun 2010
Posts: 64
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Thanks for the replies!
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