cooltools 0.3.0

Analysis tools for genomic interaction data stored in .cool format

cooltools

The tools for your .cool's

Calling compartments

To call compartments, use cooltools to calculate the first three eigenvectors across the matrix.

    cooltools call-compartments ${fullfile}::/resolutions/100000 --out-prefix $filename;

Sample output:

chrom   start   end     E1      E2      E3
1       0       100000
...
1       3000000 3100000 3.009943538549052       2.762190276669322       0.13578728460826148
...