Meaning of -n and -Q
The -n flag limits the number of results reported, not the number of alignment results. Suppose you specify "-n 1", and GSNAP finds no alignments to the genome. Then the result would contain 0 hits, obviously. Likewise, if GSNAP finds 1 hit in the genome, the result would contain that one hit. But if GSNAP found multiple hits, then the "-n 1" flag would constrain the results to a single one.
To find uniquely matching hits, you would need to add the "-Q" or "--quiet-if-excessive" flag. With "-n 1" and that flag, if GSNAP found multiple hits, then it would pretend that it really found no (unique) hits to the genome, and report no hits.
I hope that makes sense. If you have other questions, you can also join the gsnap-users mailing list at EBI.
Tom
The -n flag limits the number of results reported, not the number of alignment results. Suppose you specify "-n 1", and GSNAP finds no alignments to the genome. Then the result would contain 0 hits, obviously. Likewise, if GSNAP finds 1 hit in the genome, the result would contain that one hit. But if GSNAP found multiple hits, then the "-n 1" flag would constrain the results to a single one.
To find uniquely matching hits, you would need to add the "-Q" or "--quiet-if-excessive" flag. With "-n 1" and that flag, if GSNAP found multiple hits, then it would pretend that it really found no (unique) hits to the genome, and report no hits.
I hope that makes sense. If you have other questions, you can also join the gsnap-users mailing list at EBI.
Tom
Comment