1.ChIP-seq analysis.Rmd

---
title: "1.ChIP-seq analysis"
author: "Hao Huang"
date: "2021/2/1"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

### 1 ChIP-seq alignment

```
bowtie -t -k 1 -m 1 -p 20 Bowtie_Index_hg19/hg19 $id --sam | samtools view -q 255 -bS - > $id.bam

```

### 2 coverage tracks

```
samtools sort -@ 40 -o ${id}.sorted.bam $id
samtools index ${id}.sorted.bam
bamCoverage --bam ${id}.sorted.bam -o ${id}.sorted.CPM.smooth.bw --binSize 50 --normalizeUsing CPM --effectiveGenomeSize 2864785220 --smoothLength 200

```

### 3 identification of chromation states

```
java -jar ChromHMM.jar BinarizeBam -b 200 hg19.chrom.sizes $bam MarkTable_H3K27ac.txt Chromatin_Bins
java -jar ChromHMM.jar LearnModel -b 200 Chromatin_Bins ChromatinStates 2 hg19

```

### 4 the density of normalized mapped reads in SEs

```
bamliquidator_batch $bam -r $SE -o $SE_density -f -e 200

```