官方參考
https://deeptools.readthedocs.io/en/develop/content/installation.html
下載安裝
- python pip 安裝
$ conda install -c bioconda deeptools
- conda 安裝
$ conda install -c bioconda deeptools
bamCoverage 介紹
此工具將讀取BAM文件，并生成bigWig或bedGraph。覆蓋率計(jì)算為每個bin的讀取次數(shù)，bin為定義的連續(xù)讀取的窗口大小。bamCoverage通過RPKM，CPM，BPM ，1x，RPGC等方法提供標(biāo)準(zhǔn)化。
ChIP-seq的用法示例
較小的bin大小用于更高的分辨率，將覆蓋范圍標(biāo)準(zhǔn)化為1x小鼠基因組大小，在標(biāo)準(zhǔn)化步驟期間排除染色體X，以及擴(kuò)展讀取：
bamCoverage --bam a.bam -o a.SeqDepthNorm.bw
--binSize 10
--normalizeUsing RPGC
--effectiveGenomeSize 2150570000
--ignoreForNormalization chrX
--extendReads
bigwigCompare 的使用
此工具根據(jù)映射的讀取數(shù)比較兩個bigWig文件。為了比較bigWig文件，將基因組劃分為相同大小的區(qū)間，然后在每個區(qū)域中計(jì)算reads，然后給出數(shù)值。該值可以比率，比率的log2值，求和或者差值。
usage: bigwigCompare
--bigwig1, -b1 Bigwig file 1. Usually the file for the treatment.
--bigwig2, -b2 Bigwig file 2. Usually the file for the control.
--binSize, -bs Size of the bins, in bases, for the output of the bigwig/bedgraph file.
--numberOfProcessors, -p
Number of processors to use. Type “max/2” to use half the maximum number of processors or “max” to use all available processors.
--outFileName, -o Output file name
--outFileFormat, -of Possible choices: bigwig, bedgraph
computeMatrix 的使用
此工具依賴于上面步驟生成的bw文件，再給出bed或者gtf文件的區(qū)域（例如TSS），計(jì)算每個基因區(qū)域的結(jié)合得分，生成中間文件用以給plotHeatmap和plotProfiles作圖。
$ computeMatrix reference-point \ # choose the mode
--referencePoint TSS \ # alternatives: TES, center
-b 3000 -a 10000 \ # define the region you are interested in
-R testFiles/genes.bed
-S testFiles/log2ratio_H3K4Me3_chr19.bw
--skipZeros
-o matrix1_H3K4me3_l2r_TSS.gz \ # to be used with plotHeatmap and plotProfile
--outFileSortedRegions regions1_H3K4me3_l2r_genes.bed
-p the number of threads
plotHeatmap
這個工具根據(jù)區(qū)域得分畫出熱圖，依賴于上面computeMatrix 產(chǎn)生的矩陣文件。
This tool creates a heatmap for scores associated with genomic regions. The program requires a matrix file generated by the tool computeMatrix.
plotProfile
$ plotProfile -m matrix.mat.gz
-out ExampleProfile2.png
--plotType=fill \ # add color between the x axis and the lines
--perGroup \ # make one image per BED file instead of per bigWig file
--colors red yellow blue
--plotTitle "Test data profile"
image
