Hi, I have a set of piRNAs in fasta format and I want to find their potential targets. According to literature nucleotides in position 1-10 in the piRNAs sequences should constitute the seed and do not tolerate any mismatch while nt 11-20 tolerate up to 3 mismatches. Bowtie can specify the length of the seed, but I'm having troubles finding the right combination of parameters to translate the piRNA target pairing logic into a single bowtie command line.
Is there any solution to get this done with a single alignment run or do I have to run a first alignment guided by the seed 1-10nt, and successively another alignment for the 11-20 region allowing for up to 3 mismatches?
Thank you in advance for your help!
3 answers
How about running the alignment tolerating 3 mismatches anywhere, and then filtering the results using the CIGAR string ? (You would need an aligner that produces CIGAR strings distinguishing matches (=) and mismatches (X); I do not remember if bowtie does).
Or maybe you can use LAST with a custom seeding scheme ?
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