-
preprocess was performed for each sample
- hicup v0.7.9
- bam to pairs and pre format with pairtools v0.3.0
- pairs to
.hicand.coolmatrix with cooler v0.8.3
-
identifying AB compartments, TADs and loops for each cell type
- AB compartment at 40kb resolution (
cooltools call-compartments) - TADs at 10kb resolution (hitad v0.4.2-r1)
- loops (mustache 2020/10/13 pt < 0.1 + Fit-Hi-C v2.0.7 fdr < 1e-6) at 1K, 2K and 4K resolution.
- AB compartment at 40kb resolution (
-
loop and AB differential analysis
- Quantitative loop differential was performed by multiCompareHiC v1.8.0 for each chromosome and correct with fdr after merging all chromosomes. The global differential loops further overlap with consensus loops merged cross cell types
- AB compartment is based on the PC1 and compared across cell types.
-
single cell RNA-seq was preprocessed with cellRanger v and analyzed with Seurat
-
deconvulution was performed using MuSiC v0.1.1
- single cell RNA-seq was preprocessed with snapTools v and analyzed with snapATAC v1.0.0