Visualization of chip SEQ data by deeptools

deepTools: tools for exploring deep sequencing data

deepTools It's a set python Tools , Especially developed for efficient analysis of high-throughput sequencing data , Such as ChIP-seq、RNA-seq or MNase-seq.

##  Before and after calculating transcription start sites 1K Of peaks Distribution situation , It can be processed in parallel , Speed up 
computeMatrix reference-point -p 2 --referencePoint TSS -b 1000 -a 1000 -R UCSC_GRCH38_refGene.bed -S chip_coverage.bw control_coverage.bw --skipZeros  -out ./TSS.computeMatrix.gz --outFileSortedRegions ./test.genes.bed

#  notes ：chip_coverage.bw control_coverage.bw   come from Macs2 result 
plotHeatmap -m TSS.computeMatrix.gz -o heatmap_TSS.pdf --zMin 0 --zMax 8 --colorMap coolwarm --missingDataColor 1

# -o (-out)  The output file , It can be  ".png", ".eps", ".pdf" and ".svg"

computeMatrix scale-regions -p 2 -S chip_coverage.bw control_coverage.bw -R UCSC_GRCH38_refGene.bed -a 1000 -b 1000 -o gene_region.computeMatrix.gz

plotHeatmap -m gene_region.computeMatrix.gz -o heatmap_gene_region.pdf --zMin 0 --zMax 8 --colorMap coolwarm --missingDataColor 1

# Parameter description ：-m Input matrix ;-o Output pdf file ;-zMin 0 --zMax 8 Are the maximum and minimum values of the heat map ;--colorMap It's a choice # Choose the heat map color type (RdBu, coolwarm  etc. , See the help document for details ). Made pdf The heat map can be directly displayed in Ai Editor .

##  Drawing only  profile
plotProfile -m TSS.computeMatrix.gz -out TSSProfile.png --numPlotsPerRow 2 --plotTitle "TSS data profile"
#  Set up profile style 
plotProfile -m TSS.computeMatrix.gz -out ExampleProfile2.png --plotType=fill --perGroup --colors red yellow blue --plotTitle "Test data profile" 

##  Drawing only heatmap
plotHeatmap -m TSS.computeMatrix.gz -out TSSHeatmap.png --colorMap RdBu --whatToShow 'heatmap and colorbar' --zMin -3 --zMax 3 --kmeans 4

##  Draw at the same time profile and heatmap
plotHeatmap -m TSS.computeMatrix.gz -o heatmap_profile.pdf --zMin 0 --zMax 8 --colorMap coolwarm --missingDataColor 1 --kmeans 4

###  Parameters  --kmeans  Number of clusters 

Reference resources ：

​​​​​​​​​​​​​http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions
 

https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html​​​​​​​