Using bowtie with different mismatch options

Question

[Varun Gupta]

Hi Everyone,

I am using bowtie1 in 2 ways on the same fastq file.

Running bowtie with these options:

1. -m 1 -v 0 --best -S
2. -m 1 -v 1 --best -S

A read with option 1 maps to a particular contig. Why does the same read does not map to same contig in 2nd case when -v 1. I am mapping to my custom based genome. In the case where I am mapping it with 1 mismatch, the read goes as unmapped. 2nd option means map a read if it has 0 mismatch or 1 mismatch.

[h.mon]

why don't you post the example you described? "-v" means "report end-to-end hits w/ <=v mismatches; ignore qualities", I suspect this particular read is not an "end to end" hit.

[Varun Gupta]

Hi,

I think I figured it out. So with -m 1 -v 1 --best -S option, the read was mapping with 0 mismatch and the same read also maps with 1 mismatch some where else, it will be reported as unmapped because of -m 1 parameter