Hello,
I am currently using MAQ to align my reads. In the SAM file, MAQ outputs the number of perfect hits (H0 flag) and the number of 1-difference hits (H1).
However, as I am interested in the number of 2-difference hits (H2), I was wondering whether there is an option in MAQ to include those in the output or alternatively another aligner that includes H2 in its output.
Thank you 4 your help!
I am currently using MAQ to align my reads. In the SAM file, MAQ outputs the number of perfect hits (H0 flag) and the number of 1-difference hits (H1).
However, as I am interested in the number of 2-difference hits (H2), I was wondering whether there is an option in MAQ to include those in the output or alternatively another aligner that includes H2 in its output.
Thank you 4 your help!