Hi-C 挂载

中文

作用：用 HiC-Pro 3.1.0 处理 Hi-C reads 生成接触矩阵，再转成 cooler .cool/.mcool 并做平衡化。 入口：reference/index.sh → hicpro.sh → cooler/matrix2cool.sh（haphic/ 为另一条挂载路线，见其 README） 输入：rawreads/ 与 config-hicpro.txt（hicpro.sh 使用）；Lotus_GifuT2T_v1.0.fasta（reference/index.sh 建索引）；HiC-Pro 矩阵树 process/hic_results/matrix/Gifu/raw/{200000,100000,40000}/Gifu_<res>.matrix 与 ..._abs.bed（在 cooler/matrix2cool.sh 中硬编码）。 输出：process/ 下的 HiC-Pro 运行树（矩阵、*_abs.bed、日志）与 Gifu_T2T.* bowtie2 索引；Gifu_200kb.cool、Gifu_100kb.cool、Gifu_40kb.cool 及平衡化后的多分辨率 Gifu.mcool。 运行：bash reference/index.sh；bash hicpro.sh；bash cooler/matrix2cool.sh 工具：bowtie2-build -f --thread 88（索引前缀 Gifu_T2T）；HiC-Pro 3.1.0 --input rawreads -c config-hicpro.txt --output process；cooler load -f coo --one-based --count-as-float、create --mode mcool、balance --ignore-diags 2 --force。

English

**Purpose**: Process Hi-C reads with HiC-Pro 3.1.0 into contact matrices, then convert them to cooler `.cool`/`.mcool` files and balance them. **Entry point**: `reference/index.sh` → `hicpro.sh` → `cooler/matrix2cool.sh` (`haphic/` is a separate scaffolding route, see its README) **Inputs**: `rawreads/` and `config-hicpro.txt` (used by `hicpro.sh`); `Lotus_GifuT2T_v1.0.fasta` (indexed by `reference/index.sh`); the HiC-Pro matrix tree `process/hic_results/matrix/Gifu/raw/{200000,100000,40000}/Gifu_.matrix` with `..._abs.bed`, hardcoded in `cooler/matrix2cool.sh`. **Outputs**: the HiC-Pro run tree under `process/` (matrices, `*_abs.bed`, logs) and the `Gifu_T2T.*` bowtie2 index; `Gifu_200kb.cool`, `Gifu_100kb.cool`, `Gifu_40kb.cool` and the balanced multi-resolution `Gifu.mcool`. **Run**: `bash reference/index.sh`; `bash hicpro.sh`; `bash cooler/matrix2cool.sh` **Tools**: `bowtie2-build -f --thread 88` (index basename `Gifu_T2T`); HiC-Pro 3.1.0 `--input rawreads -c config-hicpro.txt --output process`; cooler `load -f coo --one-based --count-as-float`, `create --mode mcool`, `balance --ignore-diags 2 --force`.

本阶段步骤

步骤	内容
HapHiC 分型挂载	—