Maq mismatch

[kylle345]

Hi,

I am currently using the match function in maq to align sequence reads to a reference genome. I want to increase the mismatch to 5 or 6 but I notice that the limit is at 3. Is there anyway around this?

thanks

[nilshomer]

Hi,

I am currently using the match function in maq to align sequence reads to a reference genome. I want to increase the mismatch to 5 or 6 but I notice that the limit is at 3. Is there anyway around this?

thanks

You will have to use a different aligner. Aligners like BFAST, BWA, bowtie, etc (bowtie is not for SOLiD) will allow you to up the sensitivity at the expense of speed.

[kylle345]

hi

Hey thanks for the reply,

I am currently using bowtie since it is one of the programs that is used by our institute. I am wondering if this is the correct line to use in order to get up to 5 mismatches. If not then how would I do this?

bowtie -y --maxbts --best -n 5 -q

[nilshomer]

Hey thanks for the reply,

I am currently using bowtie since it is one of the programs that is used by our institute. I am wondering if this is the correct line to use in order to get up to 5 mismatches. If not then how would I do this?

bowtie -y --maxbts --best -n 5 -q

Looks like the "-n" option can only range from 0-3.

  -n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)

PM Ben Langmead or post a new thread asking how to do this with bowtie. Alternatively, you can ask your institution to use BFAST, which allows you to a priori tune for sensitivity including indels. Admittedly I am the author for the latter.