We have a 23 nucleotide CRISPR target sequence of which I would like to find out if it also present in other locations in the genome.
The sequences directs a CRISPR RNA construct to introduce a indel mutation in the genome and we would like to make sure that there is only one target loci. There is also one N in the nucleotide sequence.
Let's say the 23 nucleotide sequence is :
GGAGCGAGCGGAGCGGTACANGG
How do I find all the loci in a genome were this sequence matches, exactly (well 1 mismatch one the N), or with say an edit distance of 2 or 3?
I tried BWA aln with a short sequence of 23 bp from the human genome with parameters -l 23 -k 2 but it didn't find back the location of the 23 bp. Does bwa work with sequences of this lenght?
I tried blast but I get back a lot of results and I can't control the max edit distance.
