Tophat And Multiple-Mapped Reads

Question

[Biomonika (Noolean)]

I would like to ask about update on this topic:

http://seqanswers.com/forums/showthread.php?t=24270

-g/--max-multihits <int>     Instructs TopHat to allow up to this many alignments to the reference for a given read, and choose the alignments based on their alignment scores if there are more than this number. The default is 20 for read mapping. Unless you use --report-secondary-alignments, TopHat will report the alignments with the best alignment score. If there are more alignments with the same score than this number, TopHat will randomly report only this many alignments. In case of using --report-secondary-alignments, TopHat will try to report alignments up to this option value, and TopHat may randomly output some of the alignments with the same score to meet this number.

What's the situation right now? Is TopHat choosing best hit randomly or is it the first location (as reported in the past by many users). Thanks a lot.

Answer 1

[Istvan Albert]

There is a discussion here: ATTENTION: bowtie2 and multiple hits

[Biomonika (Noolean)]

Thank you. I came across these posts but I could not find the update (discussion is 5 months old).