Question: Tophat2 uniquely maping problem
0
gravatar for xuchuan
3.6 years ago by
xuchuan0
xuchuan0 wrote:

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

rna-seq • 722 views
ADD COMMENTlink modified 3.6 years ago by Benn7.9k • written 3.6 years ago by xuchuan0
0
gravatar for Benn
3.6 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

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.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Benn7.9k
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