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Old 08-08-2009, 08:46 AM   #1
kylle345
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Default Maq mismatch

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
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Old 08-08-2009, 01:50 PM   #2
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Originally Posted by kylle345 View Post
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.
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Old 08-08-2009, 04:16 PM   #3
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Default 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
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Old 08-08-2009, 04:30 PM   #4
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Originally Posted by kylle345 View Post
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.
Code:
  -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.
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