Gallery

<img src="https://raw.github.com/fidelram/deepTools/master/gallery/hm_TATA_thumb.png"/ Title="Heatmap of TATA scores around mouse gene TSS">

<img src="https://raw.github.com/fidelram/deepTools/master/gallery/hm_GC_thumb.png"/ Title="GC content for fly and mouse genes">

<img src="https://raw.github.com/fidelram/deepTools/master/gallery/hm_CpG_thumb.png"/ Title="GC content for fly and mouse genes">

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DNase accessibility at enhancers in murine ES cells

<img src="https://raw.github.com/fidelram/deepTools/master/gallery/hm_DNase.png"/ Title="Heatmap of TATA scores around mouse gene TSS">

Fast Facts
computeMatrix mode	reference-point
regions file	BED file with typical enhancer regions from Whyte et al., 2013
signal file	bigWig file with DNase signal from UCSC
heatmap cosmetics	labels, titles, color for missing data was set to white, heatmap height

Command

$ deepTools-1.5.7/bin/computeMatrix reference-point \
 -S DNase_mouse.bigwig \
 -R Whyte_TypicalEnhancers_ESC.bed \
 --referencePoint center \
 -a 2000 -b 2000 \ ## regions before and after the enhancer centers
 -out matrix_Enhancers_DNase_ESC.tab.gz 

$ deepTools-1.5.7/bin/heatmapper \
 -m matrix_Enhancers_DNase_ESC.tab.gz\
 -out hm_DNase_ESC.png \
 --heatmapHeight 15  \
 --refPointLabel enh.center \
 --regionsLabel enhancers \
 --plotTitle 'DNase signal' \

TATA

<img src="https://raw.github.com/fidelram/deepTools/master/gallery/hm_TATA.png"/ Title="Heatmap of TATA scores around mouse gene TSS">

GC content

CpG methylation

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[read]: https://github.com/fidelram/deepTools/wiki/Glossary#terminology "the DNA piece that was actually sequenced ("read") by the sequencing machine (usually between 30 to 100 bp long, depending on the read-length of the sequencing protocol)" [input]: https://github.com/fidelram/deepTools/wiki/Glossary#terminology "confusing, albeit commonly used name for the 'no-antibody' control sample for ChIP experiments"