Missing some exact match for long reads

tingchenlab / PerM

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Missing some exact match for long reads #30

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago

The reason for this is limited by the size of exact hit, which was 199 in 
version of 0.2.9.4 or before. In 0.2.9.4, you can enlarge the number of matches 
by using -k 1000, which allow 1000 alignments per read. Note -k is a little 
different from -k doesn't "exclude" reads which have more alignment than k. It 
keeps and output the best k alignments, although there could be more.

Original issue reported on code.google.com by Chen.Yan...@gmail.com on 8 Jun 2010 at 5:48

GoogleCodeExporter commented 9 years ago

The default will still be -k 200. Users can pick 1000 as the maximum buffer 
size.

Original comment by Chen.Yan...@gmail.com on 8 Jun 2010 at 5:49