Skip to content
describes how we derive mappability data of reference genome using gem tools
Python
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
Scripts
hg38.50mer
README.md

README.md

Calculate Reference Mappability

To calculate reference mappability.

hg38 50mers

gem-indexer -i hg38.fa -o hg38
gem-mappability -I hg38.gem -l 50 -o hg38.50mer -T 8
gem-2-wig -I hg38.gem -i hg38.50mer.mappability -o hg38.50mer
wigToBigWig hg38.50mer.wig hg38.50mer.sizes hg38.50mer.bw
bigWigToBedGraph hg38.50mer.bw  hg38.50mer.bedGraph
bedGraphTobed hg38.50mer.bedGraph hg38.50mer.Excludable.bed 0.33 hg38.fa hg38.Excludable.Delly.bed

GRCh37 25mers

gem-indexer -i human_g1k_v37.fasta -o human_g1k_v37
gem-mappability -I human_g1k_v37.gem -l 25 -o human_g1k_v37.25mer -T 8
gem-2-wig -I human_g1k_v37.gem -i human_g1k_v37.25mer.mappability -o human_g1k_v37.25mer
wigToBigWig human_g1k_v37.25mer.wig human_g1k_v37.25mer.sizes human_g1k_v37.25mer.bw
bigWigToBedGraph bigWigToBedGraph human_g1k_v37.25mer.bw  human_g1k_v37.25mer.bedGraph
bedGraphTobed human_g1k_v37.25mer.bedGraph human_g1k_v37.25mer.Excludable.bed 0.33 human_g1k_v37.fa human_g1k_v37.25mer.Excludable.Delly.bed
You can’t perform that action at this time.