Bowtie2 - Force alignment of terminal mismatches

Question

[timothyjoncooper]

When using end-to-end global alignment within Bowtie2, how does it handle terminal (5'/3') mismatches? For example:

REF

5'-205-GATCAAC

READ

5'-CATCAAC

Is there a way to force alignment and have Bowtie2 report the mapped coordinates in such a way to preserve the exact position of the 5' end as if the mismatch did not exist in the read? In the above example this would mean reporting that the read maps to position 205-211, rather than 206-211.

Answer 1

[Brian Bushnell]

I assume that Bowtie2 would do what you want correctly in end-to-end mode, since that's the definition of a global alignment. Assuming that your other parameters (like seed length) are set correctly, since generally aligners don't look for 6bp seed matches.

If you run BBMap with the k=6 flag (forcing length-6 seeds) it will give you the full alignment. However, bear in mind that aligners need correctly-formatted input, unlike what you posted. For example

REF

>5'-205-
GATCAAC

READ

>5'-
CATCAAC

This is correct Fasta format.