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?
1 answer
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.
Log in to answer this question.
-
Rsubread align maximum nthreads
written by Rajesh •
-
small RNA seq data from human cell line only give me 0 counts
written by leandroteixeira •
-
Help with Tophat2 run
written by Neu •
-
BBDuk Warning! "A KMER OPERATION WAS CHOSEN BUT NO KMERS WERE LOADED"
written by jerrywu1987 •
-
bowtie: poor mapping with high quality reads
written by chrisclarkson100
-
BWA mapping - only mapped the part of the reads, why?
written by gerberd1990 •
-
Phd Student working on microRNAs
written by anna.coenenstass •
-
SOLiD reads unreadable to Bowtie after unpacking from .sra archive [still open]
written by biostart
-
Tophat prep_read error
written by Yuka Takemon •
-
DSK ignores abundance-max
written by oiz67311 •
