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Old 11-07-2009, 04:06 PM   #1
Victory
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Default BWA input problem

Hi,
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.
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Old 11-08-2009, 05:47 AM   #2
dawe
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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]

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Old 11-08-2009, 06:54 AM   #3
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OMG Thank you.
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