Hi, I am working with human Hi-C data and want to aggregate the signal between PRC2, CTCF, or RAD21 peaks. I only managed to do this plot for PRC2 because I found a tip in the HICExplorer tutorial and used only interactions which were longer than the average human TAD size (~1600000). However, I struggle to get any signal for CTCF or RAD21 peaks (only background). I tried to use different datasets for the same cell type (both Hi-C and Chip-seq) and it did not help.
Could you suggest whether there are any particular filtering steps that should be applied to CTCF or RAD21 or any settings which I should apply in the tool itself? i.e. looking for TAD boundaries ChIP-seq. or using interactions between 200000-1000000 bp.
I did not find any particular tutorial on this and I am new to Hi-C data. Thus, working with Hi-C data is not intuitive for me. Could suggest any source where I can find a tip on these plots or give a suggestion yourself?
Hi, I am working with human Hi-C data and want to aggregate the signal between PRC2, CTCF, or RAD21 peaks. I only managed to do this plot for PRC2 because I found a tip in the HICExplorer tutorial and used only interactions which were longer than the average human TAD size (~1600000). However, I struggle to get any signal for CTCF or RAD21 peaks (only background). I tried to use different datasets for the same cell type (both Hi-C and Chip-seq) and it did not help.
Could you suggest whether there are any particular filtering steps that should be applied to CTCF or RAD21 or any settings which I should apply in the tool itself? i.e. looking for TAD boundaries ChIP-seq. or using interactions between 200000-1000000 bp.
I did not find any particular tutorial on this and I am new to Hi-C data. Thus, working with Hi-C data is not intuitive for me. Could suggest any source where I can find a tip on these plots or give a suggestion yourself?