Hi,
In Bowtie2 the -m option of Bowtie is deprecated. In the new versions of Bowtie2 (Beta7) they deprecated also the -M flag. It is not clear to me how to get now a "unique alignment" (namely, I want that a hit will be reported if and only if it is aligned exactly once to the reference according to my running parameters).
Thanks,
Eran
In Bowtie2 the -m option of Bowtie is deprecated. In the new versions of Bowtie2 (Beta7) they deprecated also the -M flag. It is not clear to me how to get now a "unique alignment" (namely, I want that a hit will be reported if and only if it is aligned exactly once to the reference according to my running parameters).
Thanks,
Eran