使用HINTATAC分析ATAC-seq的footprint和差异motif

 官网链接：Configuration of Genomic Data — RGT documentation

首先安装工具包，按照官网说明安装即可，需要注意的是，现在的RGT仅支持python3版本

（我以为我用3.9版本的python也可以，但是出了很多问题，建议使用3.7版本python）

这里建议可以创建一个3.7版本python的虚拟环境：

conda create -n hintatac python=3.7.7 #创建环境
conda activate hintatac #激活环境
conda deactivate #退出环境

然后按着官网代码安装，安装成功会显示successful！ 

pip install --user cython numpy scipy
pip install --user RGT --no-binary RGT

linux输入rgt-hint会显示使用说明 

usage: rgt-hint [-h] [--version]
                {footprinting,differential,plotting,training,estimation,evaluation,evidence,tracks}
                ...

positional arguments:
  {footprinting,differential,plotting,training,estimation,evaluation,evidence,tracks}
                        Commands:
    footprinting        detect footprints based on reads.bam and regions.bed
    differential        perform differential analysis based on footprints of
                        two conditions
    plotting            generate plots based on input
    training            train Hidden Markov models
    estimation          estimate sequence specific bias
    evaluation          evaluate the predicted footprints based on ChIP-seq
                        data
    evidence            create evidence file based on motif matching results
                        and ChIP-seq data
    tracks              create wig track file for visualization

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

 

接下来下载需要的基因组文件

cd ~/rgtdata
python setupGenomicData.py --all #下载hg19, hg38, mm9, mm10, zv9, and zv10

cd ~/rgtdata
python setupGenomicData.py --hg38 #仅下载hg38

可以创建一个文件夹用来储存footprint，然后继续：

rgt-hint footprinting --atac-seq --paired-end --organism=hg38 --output-prefix=name
A.bam A.bed #以我的ATAC数据为例，使用了双端等参数

后续再更新