Kmers unique mapping

Question

[enee]

Hi, I am trying to get the kmers that are uniquely located within my region of interest on the genome. I got with KMC lists of kmers in my range (I tried different lengths) and now I would like to use this multi-fasta list to align them in GRCH38 and see if they map only there or also elsewhere. I am trying to do the alignment with Bowtie because it works better with short alignments (I have kmers of max 35 bp). Once I get my .sam file with the alignment how can I identify which kmers in my list map only in my range and which map elsewhere and where?

Answer 1

[colindaven]

There is a tool for this called Genmap https://github.com/cpockrandt/genmap

It will compute mappabilty and unique regions across your genome of interest and supply results in standard formats like bedgraph and wig.

Bedgraph can be computed to bigwig and viewed in eg IGV in your region, or maybe also viewed directly.

[enee]

Thank you I'll take a look!