Getting End Location of Alignment from Bowtie 2

I was wondering if anyone knows of a good way to figure out the end location of an alignment from a Bowtie search. I first attempted to use the CIGAR string but getting the length that corresponds to returns the length of the query sequence which is not what I'm looking for. Thanks!

bowtie

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updated 7.2 years ago by Biostar

• written 7.3 years ago by eholleman12 •

but getting the length that corresponds to returns the length of the query sequence which is not what I'm looking for

What does that mean? Where is the problem?

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written 7.2 years ago by ATpoint

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