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
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