Bowtie2 adds insertions instead of allowing extention

Question

[chrisgr]

Say, I'm aligning, with Bowtie2 default settings, this short read:

>read
AGTGATCAGTGGTACACCATGTACGAATTCTCGCCTGCGAGACGA

to this short reference:

>oligo40
AGTGATCAGTGGTACACCATGTACGAATTCTCGCCTGCGA

The read is a bit longer than the reference. The problem: Bowtie aligns it resulting in this CIGAR string: 36M5I4M Which looks like:

reference:AGTGATCAGTGGTACACCATGTACGAATTCTCGCCT     GCGA
read:     AGTGATCAGTGGTACACCATGTACGAATTCTCGCCTGCGAGACGA

Bowtie2 'made up' an insertion only for the purpose to fit the whole read on the reference. But I want to allow for the read to extend the reference (perhaps assign a penalty to it, but not throw in a insertion just like that). How do I do that? Can't seem to find it anywhere.

Many thanks in advance!

[h.mon]

Doesn't seem bowtie2 is the correct tool for this task. What exactly are you trying to accomplish? If you are trying to extend the reference with reads, you can try tadpole.sh from the BBTools / BBMap package suite.

[GenoMax]

Don't know if you are able to use an alternate aligner but bbmap.sh from BBMap suite aligns the data soft-clipping the not matching part like this

read    0       oligo40 1       30      40=5S   *       0       0       AGTGATCAGTGGTACACCATGTACGAATTCTCGCCTGCGAGACGA   *       NM:i:0  AM:i:30