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Layla 06-02-2009 03:09 AM

maq map merge

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

The total reads in 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 if there is more than one alignment at a certain position does maq mapmerge only take the best qaulity?



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