deeptools 用法

原文参考 [ydchen] (http://www.biotrainee.com:8080/thread-1566-1-1.html)

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]

参考 第二个： https://weiwenku.net/d/101427044

我的

avgprof ye.liu$ computeMatrix reference-point --referencePoint TSS -b 3000 -a 3000 -R ~/Desktop/RefSeq_Genes.dms -S /Users/ye.liu/Documents/OA_Manuscript/data/bds/P1.oLT.trim.nodup.tn5_pooled.pf.pval.signal.bigwig  /Users/ye.liu/Documents/OA_Manuscript/data/bds/P1.iMT.trim.nodup.tn5_pooled.pf.pval.signal.bigwig -o matrix1_test_TSS.gz  --outFileSortedRegions regions1_test_genes.bed

这个跑了很久，

avgprof ye.liu$ plotProfile -m matrix1_test_TSS.gz -out test.pdf