#345 Bowtie changing ambiguous letters to "A"

[Constantine Chrysostomou]

I have noticed an odd occurrence when running Bowtie and I am not sure if it is intentional. I have read sequences which contain ambiguous characters that are not N (i.e. K to represent G or T).

The problem is that when I run bowtie on these read sequences, the sequence column in the SAM file changes the ambiguous character (i.e K) into A everytime.

Is there a way to suppress this?

[Val]

Yes, with the exception of 'N' bowtie does not take into consideration ambiguous characters in places where sequence operations are required. However, this behavior looks somehow like a bug to me and afaik it was not intended to behave as such. I will consult with our team and let you know if there is a bowtie2 specific work around besides preprocessing the reads before and after passing them to bowtie2.

thanks,
Val

[Val]

We fixed this in the next release. Transforming to As was clearly a mistake. The unknown chars should be translated into Ns, as bowtie2 will consider them Ns anyway for the purpose of alignment.