Hi-C aggregation plot | ARA | PE-Scan
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11 weeks ago
Argonaut • 0

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 tip in 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.

I also tried to use HICExplorer and GENOVA. (have some problems installing coolpuppy)

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 a 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?


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