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bowtie mismatch 0 alignment output

Hello there!

I'm a little confused with my output from bowtie (not bowtie2) and hoping someone may be able to clarify stuff for me. For my bowtie command I selected no mismatches using the flag -v 0. However, when I look at the output, many alignments in my sam file have XM:i:3 i.e. 3 mismatches in the alignment.

If anyone could please explain why the alignments have mismatches if I selected no mismatches in the command line it would be a great help!

Thanks

sequencing bam sam bowtie rna-seq
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updated by feng10749 • feng10749 • written by kb_93 • kb_93

First of all, why not bowtie2?

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written by Arsenal • Arsenal

I'm aligning small RNAs, so bowtie is more appropriate

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written by kb_93 • kb_93

Understood. I think you really should add that information to the post. About the mismatches. check this similar but really old post and this not that old one

There are many other posts and I won't stress showing you al of them, instead, you can google around. Good luck

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written by Arsenal • Arsenal

1 answer

Hi, I‘ve encountered the same question when I aligned my sRNA data using bowtie, and I found that the XM: i: N flag in the output of bowtie actually doesn't represent the number of mismatches, the manual of bowtie says it represents the number of the valid alignments: when there is no alignment, <N> = 0; when -m is specified, <N> = m + 1, which means there are at least that many valid alignments; and when -m is not specified, <N> = the number of alignments +1.

Reference: https://bowtie-bio.sourceforge.net/manual.shtml#default-bowtie-output

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written by feng10749 • feng10749

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