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Old 11-18-2011, 12:47 AM   #1
jay2008
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Location: Australia

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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?

thanks
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Old 05-30-2012, 05:46 AM   #2
blanco
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Default

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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