I performed compartment analysis using dcHiC and homer's runHiCpca.pl respectively. However, in homer, I used the -active <peak/BED file> option to incorporate the broad peaks obtained from my ATAC data. In the end, I found that there seemed to be some contradictions in the identification of AB compartments between dcHiC and homer, and the switch regions identified by dcHiC appeared to be missing in homer.
Thank you
best
I performed compartment analysis using dcHiC and homer's runHiCpca.pl respectively. However, in homer, I used the -active <peak/BED file> option to incorporate the broad peaks obtained from my ATAC data. In the end, I found that there seemed to be some contradictions in the identification of AB compartments between dcHiC and homer, and the switch regions identified by dcHiC appeared to be missing in homer.
Thank you
best