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figure out why tophat includes so many seconday reads #648

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
and remove if possible.

Original issue reported on code.google.com by zack...@gmail.com on 14 Jan 2014 at 10:12

GoogleCodeExporter commented 8 years ago 
its because the default is to keep up to 20 alternative hits.

we decided to NOT change the default behavior without good cause.

Original comment by zack...@gmail.com on 16 Jan 2014 at 12:01

GoogleCodeExporter commented 8 years ago 
Might be interesting sometime to remove the max just for one sample and see
how many more mappings we get.  So many seem to go to at least 20 places
(at least in a bad libe)--what can they go up to?  50, 100, 1000?  The
genome is a crazy place!

Original comment by cmnico...@gmail.com on 16 Jan 2014 at 12:04

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 22 Jan 2014 at 12:37