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Victory 11-07-2009 05:06 PM

BWA input problem
I am a new user for BWA and I have problem with input file. I saw in the manual that I need to put arguement in <out.sai>in aln step and <in.sai> in samse step. I cannot distinguish between in.sai and out.sai here. Are there any one know about this? Thank you.

dawe 11-08-2009 06:47 AM

AFAIK out.sai and in.sai are the same file...

bwa aln [ref] [seq] > file.sai
bwa samse [ref] [file.sai] [seq]

or, better,

bwa aln [ref] [seq] | bwa samse [ref] - [seq]


Victory 11-08-2009 07:54 AM

OMG Thank you.

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