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-   -   how to determine strand from tophat output for paired-end RNA-seq data (http://seqanswers.com/forums/showthread.php?t=15616)

jay2008 11-17-2011 11:47 PM

how to determine strand from tophat output for paired-end RNA-seq data
 
I used tophat to map paired end seq data xxx.1.fq and xxx.2.fq.
from the output file, I found most of reads are paired. the flags usually are
163 - 83
355 - 403
99 - 147
....
my question is:
how to determine the pair is from "+" strand or "-" strand?

thanks

blanco 05-30-2012 04:46 AM

You probably have figured something out by now but still:
tophat now has a '-library--type' option which can tell you from which strand the read came from (assuming the library is strand specific).


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