BWA input problem

[Victory]

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.

[dawe]

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]

d

[Victory]

OMG Thank you.