2025年03月27日
先看一篇高分文章：Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer
With the use of the ChromHMM algorithm,14 we trained a 10-state, 12-state and 15-state model (for
samples having all the six marks; online supplemental table S1)
consisting of combinatorial patterns of specific histone modifications known as chromatin states, which are linked with the
transcriptional output of the associated genomic loci and regulate the recruitment of various components of the transcriptional
machinery. We chose a 10-state model for in-depth investigation
because it represented biologically interpretable combinatorial
patterns that were not repetitive or ambiguous (figure 1A and
online supplemental figure S1A). We annotated these chromatin states based on the content of each state and its average
relative distribution around known genomic features (online
supplemental figure S1B).
因为一个基因组locus可以有很多歌histone state，某些histone mark之间具有协同或拮抗作用，所以这里相当于做个一个（maybe线性）变换，输入是所有histone mark，输出是统一的chromatin state。
如果有超过5个以上的histone marks，那这个就属于必做的分析。
代码
ChromHMM.sh BinarizeBam -gzip -b 200 -f 2 -paired chrom.sizes.hg38 3.bam design_sheet.txt binarization
# 容易爆内存，我猜一个线程会占用很多内存 default_jvm_mem_opts="-Xms20m -Xmx30g" ChromHMM.sh LearnModel -gzip -d 0.001 -color 0,0,255 -p 4 -i chrhmm binarization learnmodel 10 hg38
参考项目：/home/zz950/projects/BAF_SOX9/diffbind/chromhmm
参考：
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