Lucky you @manojmumar_bhosale I worked on similar problem recently and therefore have the bash script you can use.
Required tools:
- GEM libary from here
-
UCSC’s wigToBigWig from here (I chose binary for Linux 64 bit, you can choose different OS)
#!/bin/bash - #=============================================================================== # # FILE: mappa_cacl.sh # # USAGE: ./mappa_cacl.sh # # DESCRIPTION: # # OPTIONS: --- # REQUIREMENTS: --- # BUGS: --- # NOTES: --- # AUTHOR: Vang Le (vql AT rn.dk) # ORGANIZATION: # CREATED: 26/02/16 01:49 # REVISION: --- # Reference: http://wiki.bits.vib.be/index.php/Create_a_mappability_track #=============================================================================== set -o nounset # Treat unset variables as an error pref="rn6.softmask.all" # should be changed reference="rn6.softmask.all.fa" # should be changed idxpref="${pref}_index" thr=20; # use 20 cores, change it to the number you want to use outmappa="rn6.mappa.tsv" # should be changed #make index for the genome gem-indexer -T ${thr} -c dna -i ${reference} -o ${idxpref} # The following calculates index and creates mappability tracks with various kmer lengths. # it may take long time to finish. # choose the right kmer length for you. for kmer in 45 50 75; do # compute mappability data gem-mappability -T ${thr} -I ${idxpref}.gem -l ${kmer} -o ${pref}_${kmer} mpc=$(gawk '{c+=gsub(s,s)}END{print c}' s="!" ${pref}_${kmer}.mappability) echo ${pref}_${kmer}"t"$mpc >> $outmappa # convert results to wig and bigwig gem-2-wig -I ${idxpref}.gem -i ${pref}_${kmer}.mappability -o ${pref}_${kmer} wigToBigWig ${pref}_${kmer}.wig ${pref}.sizes ${pref}_${kmer}.bw done
Script from @biocyberman is great. For those who are still looking for this, here are steps:
1) Get the reference hg38 genome, in uncompressed fasta format (obviously)
2) Get the ‘gemtools’:
a) SourceForge –> Version 2, pre release
or
b) GitLab –> Version 1.7
3) Create the index of the genome by using following command:
gemtools index -i <referenceGenome.fasta:PATH> -t <NumberOfThreadsToUse:int>
e.g.:
gemtools index -i GRCh38.p12.fasta -t 40
4) Once, the index is made, generate the mappability data like:
gem-mappability -I <referenceGenome_index.gem:PATH> -l <K-mer_length:int> -o <output_name.gem:PATH>
e.g.: For 100 mer, the command will be:
gem-mappability -I GRCh38.p12.gem -l 100 -o GRCh38_mappability_100mer.gem
The complete guide is available at this wiki
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