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Old 04-22-2009, 02:42 PM   #8
Layla
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Location: London

Join Date: Sep 2008
Posts: 58
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I think q -1 sounds like a valid option. Or you can simple grep for reads with the 0 flag and remove them before down-stream processing.

Whilst on this note, anyone used SISSR instead of Maq? And if so, any thoughts on what to do with the data after SISSR gives 80,000 potential binding sites with p values < 0.001, high tag counts and fold changes?

The data never simplifies!!!!

L
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