Dave Gerrard | 25 Jan 13:02 2013
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BitSeq: Required input for 3' bias correction on transcripts.

I have RNAseq data generated from poly-A capture RNAs.  There appears to be
a strong 3' bias to the mapped reads but the library prep was NOT strand
specifc. I would like to correct for the positional bias in the mapped
reads and  Bitseq has a 'uniform' parameter which can be set to 'FALSE' if
reads are not uniform.  Please can you tell me if this requires 'stranded'
mapped read information (as per the cufflinks manual) or whether It will
work without knowing the source strand?

Thanks,
Dave Gerrard
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