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-   -   maq map merge (http://seqanswers.com/forums/showthread.php?t=1861)

Layla 06-02-2009 03:09 AM

maq map merge
 
Hi

I have 2 .map files from two paired end alignments using maq map.
Merged them using ./maq mapmerge expt1.map expt2.map output.map

The total reads in output.map should be 18 million (expt1 + expt2) but is only 12 million. Any idea as to what happened to the remaining 6 million reads?

For example, an alignment at chr 1 position 1 should appear a total of 3 times in the merged output file, but is only there once. Yes the flag is poor in 2 of the positions..so if there is more than one alignment at a certain position does maq mapmerge only take the best qaulity?

Cheers

L


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