Dear all,

the option specified for the number of hits in a SAM output, NH, is amazingly missing from the two most popular aligners (namely BWA and Bowtie). However, Tophat2 reports the NH flawlessly, therefore there must be a way to run Bowtie(2) with an option to generate this report.

So far, too much of the community is resorting to the samtools view -q3 trick, which is able to extract alignments with a mapping quality below 50% (by definition, a multiple hitting read will have all its n equally good alignments with a score of at most 1/n).

Thanks for any hints. I hope this post will become viral.

Federico Giorgi (CUMC) & Davide Scaglione (IGA)

the option specified for the number of hits in a SAM output, NH, is amazingly missing from the two most popular aligners (namely BWA and Bowtie). However, Tophat2 reports the NH flawlessly, therefore there must be a way to run Bowtie(2) with an option to generate this report.

So far, too much of the community is resorting to the samtools view -q3 trick, which is able to extract alignments with a mapping quality below 50% (by definition, a multiple hitting read will have all its n equally good alignments with a score of at most 1/n).

Thanks for any hints. I hope this post will become viral.

Federico Giorgi (CUMC) & Davide Scaglione (IGA)

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