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Old 11-18-2011, 12:47 AM   #1
Location: Australia

Join Date: Sep 2010
Posts: 44
Default 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?

jay2008 is offline   Reply With Quote
Old 05-30-2012, 05:46 AM   #2
Location: Iceland

Join Date: Apr 2012
Posts: 28

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).
blanco is offline   Reply With Quote

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