Detect nucleosome depleted region

Detect nucleosome depleted region

The ndr subcommand in BISCUIT detects nucleosome depleted region (NDR) from Nucleosome Occupancy and Methylome Sequencing (NOMe-seq) data. To call nucleosome depleted region, one issues

biscuit vcf2bed -t gch -c HCT116.vcf.gz | biscuit-develop ndr -b - -o OUT

which infer on each base of GCH context a state whether the region is depleted of occupancy.

...
chr18   11566   1
chr18   11574   1
chr18   11575   1
chr18   11687   1
chr18   11704   0
chr18   11705   0
...

-c option further collapse the state calls into regions:

biscuit vcf2bed -t gch -c HCT116.vcf.gz | biscuit-develop ndr -b - -o OUT

outputs regions spanned by consecutive depletion regions.

...
chr18   11515   11516
chr18   11524   11687
chr18   11902   11945
...