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Old 11-18-2010, 07:46 PM   #1
MBekritsky
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Location: CSHL

Join Date: Nov 2009
Posts: 15
Default MAQ simulated read header names

Hi,

I'm using MAQ to simulate reads and I was hoping someone could shed some light on how the read names are generated. It looks as though the name is something like:
(coordinate name)_(start position in the coordinate)_(stop position in the coordinate)_(hexadecimal number for the read)/(1/2)
Since the reads are simulated as mate pairs, (stop position - start position + 1) is the outer distance of the insert sizes, which will vary based on the desired mean outer distance of insert sizes and its standard deviation. I looked around MAQ's documentation to see if they described the method, but I had no luck. Does anyone happen to know if this is the naming convention?

Thanks!
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