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Old 06-22-2011, 05:13 AM   #5
CNVboy
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Location: boston

Join Date: Jun 2011
Posts: 27
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THanks everyone.

I think the core question is: how can we guarantee the quality of the generated .sai, .sam file? How do you know the programming at this step is complete? Just look at the size of files; or ,say judge the quality of .sai file by checking if it can produce .sam file?

For example, some of my .sai file looks good size-wise, but somehow cannot produce .sam file with correct size (.sam file is only 8.0kb); then I just reproduce .sai file, and it can generate .sam file with correct size.

Also, seems BWA returns exit codes; can we use this as the sign of completeness of each step? And try to make it like, command 2 will execute only if command 1 runs successfully

Last edited by CNVboy; 06-22-2011 at 05:19 AM.
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