Can any one advise what -g option is doing is it now giving in addition to 40, 20 alignments ar ereported or it is doing something to multihits problem.
Thanks.
Honey
-
TopHat multi hits
In addition to reporting the best (or primary) alignments (the original TopHat behavior), TopHat 2 can report the secondary alignments up to 20 (the default) paired or single alignments (see --report-secondary-alignments and -g/--max-multihits)
Can any one advise what -g option is doing is it now giving in addition to 40, 20 alignments ar ereported or it is doing something to multihits problem.
Thanks.
Honey
-
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