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bowtie options for exact match with reference short sequence

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?

bowtie exact option
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updated by Ram Ram • written by manekineko manekineko

Just to make sure bowtie or bowtie2?

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written by thackl thackl

bowtie

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

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written by manekineko manekineko

1 answer

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

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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