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Old 10-02-2012, 07:12 AM   #1
dekontrol
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Default Paired-end strand specific RNA-seq

Hi all,

I have aligned paired-end RNA-Seq data generated with a strand-specific library (on Illumina HiSeq).

Is possible to known how to assign the pairs to the RNA strand from which was generated from the SAM file?

In other word I am looking for a way to generate two different bigWig files: one with the signal coming from one strand, and one with the signal coming from the other strand..

Thanks very much!

Best,
albert
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Old 10-07-2012, 12:14 AM   #2
Torst
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Did you align them with strand-specific options enabled?
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Old 10-07-2012, 12:22 AM   #3
dekontrol
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I am using an aligner which don't have this option..(novoalign).. However if this is essential I can try other aligners like TopHat..
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