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

The following image demonstrates that enhancer regions are typically small stretches of highly accessible chromatin. Yellow and blue color tiles indicate large numbers of reads that were sequenced, black spots indicate missing data points. An appropriate labeling of the y-axis was neglected.

<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 (download here)
signal file	bigWig file with DNase signal from UCSC
heatmap cosmetics	labels, titles, 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">

Fast Facts
computeMatrix mode	reference-point
regions file	BED file with all mouse genes (from UCSC table browser)
signal file	bigWig file of TATA psem scores
heatmap cosmetics	color scheme, labels, titles, color for missing data was set to grey, heatmap height

GC content

<img src="https://raw.github.com/fidelram/deepTools/master/gallery/hm_GC.png"/ Title="Heatmaps of GCcontent for fly and mouse genes">

Fast Facts
computeMatrix mode	scale-regions
regions files	BED files with mouse and fly genes (from UCSC table browser)
signal file	bigWig files with GC content
heatmap cosmetics	color scheme, labels, titles, color for missing data was set to white, heatmap height

CpG methylation

<img src="https://raw.github.com/fidelram/deepTools/master/gallery/hm_CpG.png"/ Title="Heatmaps CpG methylation percentages around the TSS of ESC-active genes">

Fast Facts
computeMatrix mode	rerence-point
regions files	BED file mouse genes expressed in ES cells
signal file	bigWig files with fraction of methylated cytosins (from Stadler et al., 2011)
heatmap cosmetics	color scheme, labels, titles, color for missing data was set to customized color, y-axis of profiles were changed, heatmap height

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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"