bowtie options for exact match with reference short sequence

Question

[manekineko]

Hi, I have bowtie with short sequences of 20nt. Is there a way to map and output a results with exact match also exact lenght e.g. searching for indentical sequences - if the reference sequence is 20nt to map and output the result with exact match and lenght 20nt, and not exact match also of 19, 18 seq?

[thackl]

Just to make sure bowtie or bowtie2?

[manekineko]

bowtie

I just want to detect the identical sequences - no mismatches and same length.

Answer 1

[Brian Bushnell]

I wrote a program called Dedupe (part of BBTools) that might accomplish what you're trying to do. It finds all exactly matching sequences. The default mode is to remove all but one copy of exactly matching sequences, but you can also tell it to remove all nonunique sequences, which allows you to do this:

dedupe.sh in=reads.fq ac=f out=a.fq
dedupe.sh in=ref.fq ac=f out=b.fq

Now a.fq and b.fq contain only 1 copy of each sequence.

dedupe.sh in=a.fq,b.fq ac=f out=unique.fq uniqueonly

unique.fq contains only sequences that are not shared between a.fq and b.fq.

dedupe.sh in=a.fq,unique.fq ac=f out=shared.fq uniqueonly

shared.fq will now contain all the sequences that are shared between a.fq and b.fq, which is hopefully what you are looking for.

For some reason Sourceforge is down right now but you can download it here:https://drive.google.com/open?id=0B3llHR93L14wTzZSMjZvdjdmYzg

[AHW]

How to tell your tool to extract only the exact matching reads. I have asked the question C: Count exact match reads in SAM file