Hi all,
I'm about to map a set of short reads after an exome capture.
I wonder if it would be worth to replace all the non-genic genomic sequences (using ucsc 'knownGene' ) with 'N'.
Wouldn't it speed up the alignment with BWA ? What would be the other possible consequences ? Has it ever been done before ?
Many thanks
Pierre
(copied from : http://biostar.stackexchange.com/questions/4413 )
I'm about to map a set of short reads after an exome capture.
I wonder if it would be worth to replace all the non-genic genomic sequences (using ucsc 'knownGene' ) with 'N'.
Wouldn't it speed up the alignment with BWA ? What would be the other possible consequences ? Has it ever been done before ?
Many thanks
Pierre
(copied from : http://biostar.stackexchange.com/questions/4413 )
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