Dear all,
I'm trying to align reads in a local mode in order to obtain the same mapping as in attached file.
I want a seed of 18 nt allowing 1 mismatches but the mapping doesn't necessarily occur in the first bases of my reads; so i try this command line in bowtie2 :
but it doesn't work
Any ideas ? is this kind of mapping possible ?
Thanks in advance for your reply.
I'm trying to align reads in a local mode in order to obtain the same mapping as in attached file.
I want a seed of 18 nt allowing 1 mismatches but the mapping doesn't necessarily occur in the first bases of my reads; so i try this command line in bowtie2 :
Code:
bowtie2 -N 1 -L 18 --local
Any ideas ? is this kind of mapping possible ?
Thanks in advance for your reply.