Map file for hg19 ; 150kmer

[ChitrArpita]

Hi,

I want to run BICSEC2 on whole genome data that aligned with NCBI37 but the paired end read length is 150bp.

[xiucz]

Hi, @ChitrArpita
You can prepare your mappability file like this.

readLength=150
gem-indexer -i ucsc.hg19.fasta -o ucsc.hg19.mappability -T 12
gem-mappability -m 2 -I ucsc.hg19.mappability.gem -l ${readLength} -o ucsc.hg19.mappability.${readLength}mer -T 12 &> ucsc.hg19.mappability.${readLength}mer.mappability.log
gem-2-wig -I ucsc.hg19.mappability.gem -i ucsc.hg19.mappability.${readLength}mer.mappability -o ucsc.hg19.mappability.${readLength}mer
wigToBigWig ucsc.hg19.mappability.${readLength}mer.wig ucsc.hg19.mappability.${readLength}mer.sizes ucsc.hg19.mappability.${readLength}mer.bw
bigWigToBedGraph ucsc.hg19.mappability.${readLength}mer.bw ucsc.hg19.mappability.${readLength}mer.bedGraph
#bedGraphTobed ucsc.hg19.mappability.${readLength}mer.bedGraph ucsc.hg19.mappability.${readLength}mer.bed 0.3

mkdir -p ucsc.hg19.${readLength}mer
cd ucsc.hg19.${readLength}mer
while read chr; do
    grep -w ${chr} ../ucsc.hg19.mappability.${readLength}mer.bedGraph | awk '$4==1 {print $2,$3}' > ucsc.hg19.${readLength}mer.${chr}.txt
done<chrName.1.txt

$cat chrName.1.txt
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY