UserContent
released
November 24th, 2020 at 5:21pm
Compartments
Methods
The workflow uses the cooltools software to call compartment signals in cis for each chromosome. A principal component analysis is performed on the matrix at 250kb resolution. The Eigenvector among the top three with highest correlation to GC content is selected and oriented such that positive values correspond to high GC.
The workflow components are pre-installed in a publicly available Docker image (4dndcic/4dn-compartments-caller:v1.2) on Docker Hub. The source code for the Docker image and the pipeline description in Common Workflow Language (CWL) can be found on 4DN-DCIC GitHub repo.