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@@ -13,7 +13,9 @@ CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from w
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* Aggregated all chromosome output into a single file for easier visualization in IGV
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* Added output in tabular .txt format at bin level for easier downstream analysis
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-### Introduction of opitimized `bin_size` selection
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+Below we introduce two of the main updates:
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+
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+### (1) Opitimized `bin_size` selection
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Due to reasons such as low data quality or large scale structrual variation, compartments can be unreliablly called at one `bin_size` (equivalent to `resoltution` in the literature) but correctly called at another `bin_size`. We added an opitimized `bin_size` selection strategy to call reliable compartments. This strategey is based on the observation from our large scale compartment analysis (https://www.nature.com/articles/s41467-021-22666-3) that, although compartments can change between different conditions, their overall correlation `cor(compartment_rank_1, compartment_rank_2)` is high (> 0.4).
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<br>
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@@ -32,7 +34,7 @@ if(bin_size==50E3) bin_sizes = c(50E3, 100E3)
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```
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Note that this strategy is currently only available for `hg19`, `hg38`, `mm9` and `mm10` genome for which we generated high quality reference compartments using Hi-C data from: GSE63525 for `hg19`, https://data.4dnucleome.org/files-processed/4DNFI1UEG1HD/ for `hg38`, GSM3959427 for `mm9`, http://hicfiles.s3.amazonaws.com/external/bonev/CN_mapq30.hic for `mm10`.
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-### Introduction of CALDER analysis for other genomes
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+### (2) Support for other genomes
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Although CALDER was mainly tested on human and mouse dataset, it can be applied to dataset from other genomes. One additional information is required in such case: a `feature_track` presumably positively correlated with compartment score (thus higher values in A than in B compartment). This information will be used for correctly determing the `A/B` direction. Some suggested tracks are gene density, H3K27ac, H3K4me1, H3K4me2, H3K4me3, H3K36me3 (or negative transform of H3K9me3) signals. Note that this information will not alter the hierarchical compartment/TAD structure, and can come from any external study with matched genome. An example of `feature_track` is given in the **Usage** section.
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Yuanlong LIU