Bowtie2 allowing mismatches syntax issue

Question

[aggiegurl2009]

Hello all. I am learning bowtie2 for a school project and I am completely new to the bioinformatics world.

What we are trying to do is allow for 3 mismatches in bowtie2 given 5 .fastq files as the input to the eventual sam file. I know I am supposed to put -v 3 somewhere in the command line code but not exactly sure. This is what I did to run it the first time with standard mismatches:

~/bowtie2-2.2.1/bowtie2 -x projectreference3 SRR072814.fastq,SRR072815.fastq,SRR072816.fastq,SRR072817.fastq,SRR072818.fastq -S <sam file name here>

If someone can help me I would greatly appreciate it.

Answer 1

[Matt Shirley]

Take a look at the Bowtie2 manual here. In beta versions of Bowtie2 there was an -M option that allowed you to specify the exact number of mismatches allowed. That option has since been deprecated and is not in the version you are using. You can adjust the mismatch penalty and, I believe, allow more mismatches during seeding, but that is all.

[aggiegurl2009]

Yes, I figured that out and think I have a solution. I appreciate your feedback. Thank you!