#deeptools安装conda install deeptoolsgtf2bed ~/gc_genome/17.Geta/1.geta/out.gtf genome.bedfor i in `cat ../samples.txt`; do echo \"bamCoverage -p 5 --normalizeUsing RPKM -b $i.last.bam -o $i.last.bw\"; done bam2bw.listParaFly -c bam2bw.list -CPU 9computeMatrix reference-point --referencePoint TSS -p 15 -b 10000 -a 10000 -R ../genome.bed -S ../*bw --skipZeros -o matrix1_test_TSS.gz --outFileSortedRegions regions1_test_genes.bedplotHeatmap -m matrix1_test_TSS.gz -out test_Heatmap.pdf --plotFileFormat pdf --dpi 720plotProfile -m matrix1_test_TSS.gz -out test_Profile.pdf --plotFileFormat pdf --perGroup --dpi 720computeMatrix scale-regions -p 150 -b 10000 -a 10000 -R ../genome.bed -S ../*bw --skipZeros -o matrix1_test_body.gz --outFileSortedRegions regions1_test_body.bedplotHeatmap -m matrix1_test_TSS.gz -out test_Heatmap.pdf --plotFileFormat pdf --dpi 720plotProfile -m matrix1_test_TSS.gz -out test_Profile.pdf --plotFileFormat pdf --perGroup --dpi 720

七、重复样品处理（至少两个生物学重复）
IDR是通过比较一对经过排序的regions/peaks 的列表，然后计算反映其重复性的值，同时得到了merge后的一致性的peaks。

for i in `cat ../../samples.txt`; do echo \"sort -k8,8nr ../$i.peaks_peaks.narrowPeak $i.peaks.narrowPeak\"; done peaks_sort.listParaFly -c peaks_sort.list -CPU 9

八、peaks注释（非模式物种）
使用GenomicFeatures包的函数制作TxDb对象：

#makeTxDbFromUCSC： 通过UCSC在线制作TxDb#makeTxDbFromBiomart: 通过ensembl在线制作TxDb#makeTxDbFromGRanges：通过GRanges对象制作TxDb#makeTxDbFromGFF：通过解析GFF文件制作TxDbgc_TxDB - makeTxDbFromGFF(\"genome.gff3\")library(clusterProfiler)library(\"ChIPseeker\")library(ChIPpeakAnno)library(GenomicFeatures)library(\"ggupset\")library(\"ggimage\")gc_TxDB - makeTxDbFromGFF(\"out.gff3\")promoter - getPromoters(TxDb=gc_TxDB, upstream=3000, downstream=3000)files = list(A_summits = \"A.peaks_summits.bed\", B_summits = \"B.peaks_summits.bed\", C_summits = \"C.peaks_summits.bed\", D_summits = \"D.peaks_summits.bed\")peakAnno - annotatePeak(files[[1]], tssRegion=c(-3000, 3000), TxDb=gc_TxDB)plotAnnoPie(peakAnno)#tiff(\"peakAnno.tiff\")#plotAnnoPie(peakAnno)#dev.off() 此方法保存的图片标注有颜色模块plotAnnoBar(peakAnno)vennpie(peakAnno)peakAnnoList 3\')\",  ylab = \"Read Count Frequency\")tagMatrixList