I am using bowtie1 in 2 ways on the same fastq file.
Running bowtie with these options:
-m 1 -v 0 --best -S
-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.