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Old 01-19-2010, 10:34 AM   #1
Location: Vienna

Join Date: Aug 2008
Posts: 11
Default TopHat: ambiguous hits are only reported for one of the two paired end reads

Hi guys,

I was just inspecting the file accepted_hits.sam from my TopHat output. TopHat per default reports as much as 40 ambiguous mapping positions for a read. That's why I wanted to find out what happens when both reads of a paired end are ambiguously mapped. It turns out that TopHat only reports the ambiguous positions for one of the two reads.

That is why I wanted to ask if someone found something similar?
If someone knows if TopHat is randomly picking one of the two?
What happens if one read is ambiguous and the other unambiguous?

TopHat seems like a neat piece of software and I really would like to use it for our RNA-seq experiment but first I need to make sure that I understand what it is doing. So I really would appreciate any help on this issues.

best ro
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