C-SCAn bedfiles

[Moonriver1988]

Hello,

I'd like to know what are the bed files in the bedlist in CSCAn? The bed files should be loop anchor, or they can be mixture of anchor and non-anchor, i.e. they can be the regions of interest through this CSCAn analysis to see whether some of these regions in A could have interaction with regions in B?

Based on "Hi-C analyses with GENOVA: a case study with cohesin variants" paper "C-SCAn builds on this by performing aggregation of pairwise combinations of two different genomic features, for instance gene promoters and distal enhancers, but excluding the homotypic pairwise combinations", and the help page of CSCAn "anchors
(Optional) A matrix with two columns containing pre-computed anchor indices. If this is set, skips calculation of anchor indices and uses this argument instead. See anchors_CSCAn()." Seems like it should work if the bed file contains both anchor and non-anchor, the C-SCAn will search for anchor. I tried to test it with H3K27ac peak and EP300 peak, but no central dot shown on the enrichment heatmap, H3K27ac and EP300 often coocupy the same location, many loops are anchored with these markers, I think it should show enrichment of the loop. Does the enrichment of the loop has to be a central dot?

How to interpret Fig. 2G, the red square in the lower left of WAPL deletion? Does this also represent enrichment of loop, increased interaction between divergent CTCF loop after WAPL deletion?

Could you help me with this? Thank you very much!

[teunbrand]

Hi there,

I'm unsure what exactly you mean with anchor and non-anchor. In the bedlist, every row from one list element acts as an anchor to pair with an anchor from every other list element (with some constraints). If you're using H3K27ac and P300 ChIPseq peaks and they co-occupy the same locations, there will be a lot of anchor pairs wherein the two anchors fall inside the same bin, which would be a location on the diagonal of the Hi-C matrix. I'm guessing this is mostly what you're looking at in your plot.

In Fig 2G WAPL KO with divergent anchors, I suspect the red square are just intra-TAD interaction that become stronger due to cohesin staying on the chromatin longer without the release factor WAPL.

[Moonriver1988]

Hello,

Thanks for your reply! I understand now. Thank you very much for your help!

[hanshanmengqi]

@teunbrand Dear developer,

Thank you for your powerful tool. Now I met a situation that show below, I used CSCAn want to check interactions between H3K27me3 and H3K27me1 in tomato. My command:

_" library(GENOVA) WT <-load_contacts(signal_path = 'HiC_WT_20000.matrix',indices_path = 'HiC_WT_20000_abs.bed', samplename= 'WT' ) K27me3 <- read.delim('.H3K27me3',header=F) K27me1 <- read.delim('.H3K27me1',header=F) out <- CSCAn(WT,bedlist = list (K27me3,K27me1)) visualise(out) "

This is result I got

But I expect result should be like this

I don't understand why the red color occurs at the bottom left and not in the center.

Thank you in advance. Best, Han