Tophat2 uniquely maping problem

Question

[xuchuan]

Hi everyone, I hava a question, when I set "-g 1" options in tophat2. Does it represent only report uniquely mapped reads or reported one alignment when multiple alignments are availbale for a read? Thank you very much

Answer 1

[Benn]

See manual (https://ccb.jhu.edu/software/tophat/manual.shtml) for your answer:

-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.