running dhHiC on nf-core hic pipeline output file

[chklopp]

Hi,

The nf-core hicpro pipeline (https://nf-co.re/hic/usage) generates compartment files :

Results are available in results/compartments/ folder and includes :
*cis.vecs.tsv: eigenvectors decomposition along the genome
*cis.lam.txt: eigenvalues associated with the eigenvectors

How can we analyze these files with dhHiC?

[jeffreygwang]

Hello! You should be able to take the eigenvectors along the genome and plug them into dcHiC with just a bit of reformatting — see this page about using existing PC's with dcHiC. You will likely be using intra as your PC type, and the replicate/sample relationships can be read about in the main README (see how to format the input file).

Before doing this, I would also check to make sure your PC's are correctly oriented (i,e. that the signs are not flipped along a particular chromosome).