Using Bowtie To Only Search In Restricted Regions

Question

[Click downvote]

I want to search the rat genome for some very short sequences, about 6-8 nucleotides in length. I'm only interested in results in the promoter or repeat masker regions. How do I restrict my search to these places? I know their locations thanks to the UCSC table browser.

Thanks.

[Sean Davis]

How many short sequences do you have? Do you need to capture mismatches, or are exact matches only in the genome acceptable?

Answer 1

[Irsan]

Then make fasta-file with all the sequences of the genome you want bowtie to align your 6-8 nucleotides to and build an index of the fasta-file. Then align your nucleotides to your custom index. See bowtie documentation how to do these things

[Click downvote]

Thank you for your answer.

My only concern is the following:

Let us say I have a genome

ACAGTACA

and I snip away the GTA part before building an index. Won't the index now tell me that the last nucleotides in the original string begin at the wrong position?

Ie original string and the corresponding index is

ACAGTACA 12345678

When I snip away GTA and index that I get

ACACA 12345

but of course, what I want is

ACACA 12378

[Irsan]

You can also convert the bases that you are not interested in to N's. So in this case convert GTA to NNN