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Old 08-26-2013, 07:35 AM   #1
Junior Member
Location: Pennsylvania

Join Date: Oct 2012
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Default Mixing strand-specific and non strand-specific reads in RNA-seq

Hi all,

We have some old RNA-seq data sequenced from non strand-specific libraries. Recently we got some new data from the same samples sequenced from strand-specific libraries. We intended to get deeper sequencing but somehow got different preparation.

Can we mix the reads and align them as all non strand-specific reads in STAR? Would it be problematic in the Cuffdiff analysis after alignment?

Thank you!
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Old 08-26-2013, 10:42 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

While it has been a while since I did so, I did not have problems mixing strand-specific and non-strand specific libraries thus making them all non-strand-specific. You lose information about the strand, of course, but nothing else.
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Old 08-27-2013, 02:39 AM   #3
not just another member
Location: Belgium

Join Date: Aug 2010
Posts: 264

And is it a good idea to perform expression analysis using both unstranded and stranded samples ? using htseq-count and DESeq for example ?
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