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发表于 2017-5-29 15:15:34 | 显示全部楼层 |阅读模式
自己看readme吧
我给出我的代码。
安装方式,见群主的生物信息学常见1000个软件的安装代码!
[Shell] 纯文本查看 复制代码
bamCompare  -b1 treatment.bam -b2 control.bam -o log2ratio.bw 
bamCoverage -b test.bam -o test.bw
## both -R and -S can accept multiple files 
computeMatrix reference-point  --referencePoint TSS   -b 10000 -a 10000    \
		-R ~/annotation/CHIPseq/mm10/ucsc.refseq.bed  \
		-S  test.bw  --skipZeros  -o matrix1_test_TSS.gz  \
		--outFileSortedRegions regions1_test_genes.bed
## 	both plotHeatmap and plotProfile will use the output from 	computeMatrix
plotHeatmap -m matrix1_test_TSS.gz  -out test.png
plotHeatmap -m matrix1_test_TSS.gz  -out test.pdf --plotFileFormat pdf  --dpi 720  
plotProfile -m matrix1_test_TSS.gz  -out test.png
plotProfile -m matrix1_test_TSS.gz  -out test.pdf --plotFileFormat pdf --perGroup --dpi 720 
multiBigwigSummary bins -b *.bw  -out scores_per_bin.npz --outRawCounts scores_per_bin.tab
multiBamSummary  bins -b *.bam  -out scores_per_bin.npz --outRawCounts scores_per_bin.tab
## both plotCorrelation and plotPCA will use the output from  multiBamSummary or multiBigwigSummary.
plotPCA -in scores_per_bin.npz  -o PCA_readCounts.png
## most of time, we don't need plotCoverage and computeGCBias,while both of them use the sorted bam file as input 
plotCorrelation -in scores_per_bin.npz  \
--corMethod pearson --skipZeros  --whatToPlot scatterplot \
-o scatterplot_PearsonCorr_bigwigScores.png 
plotCorrelation -in scores_per_bin.npz  \
--corMethod pearson --skipZeros    \
--whatToPlot heatmap --colorMap RdYlBu --plotNumbers \
-o heatmap_SpearmanCorr_readCounts.png   \
--outFileCorMatrix SpearmanCorr_readCounts.tab
# [url]https://deeptools.readthedocs.io/en/latest/content/tools/multiBigwigSummary.html[/url]
# [url]https://deeptools.readthedocs.io/en/latest/content/tools/plotPCA.html[/url]
# [url]https://deeptools.readthedocs.io/en/latest/content/tools/plotCorrelation.html[/url]



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