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, regions sorted ascendingly, only showing heatmap + colorbar

The bigWig file of motif scores was generated using the TRAP suite.

$ deepTools-1.5.7/bin/computeMatrix reference-point \
 -S TATA_01_pssm.bw \
 -R RefSeq_genes.bed \
 --referencePoint TSS \
 -a 100 -b 100 \
 --binSize 5 \

$ deepTools-1.5.7/bin/heatmapper \
 -m matrix_Genes_TATA.tab.gz  \
 -out hm_allGenes_TATA.png \
 --colorMap hot_r \
 --missingDataColor .4 \
 --heatmapHeight 7 \
 --plotTitle 'TATA motif' \
 --whatToShow 'heatmap and colorbar' \
 --sortRegions ascend

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

Fly and mouse genes were scaled to different sizes due to the different median sizes of the two species' genes (genes of D.melanogaster contain much fewer introns and are considerably shorter than mammalian genes). Thus, computeMatrix had to be run with slightly different parameters while the heatmapper commands were virtually identical (except for the labels).

$ deepTools-1.5.7/bin/computeMatrix scale-regions \
 -S GCcontent_Mm9_50_5.bw \
 -R RefSeq_genes_uniqNM.bed \
 -bs 50 
 -m 10000 -b 3000 -a 3000 \ 
 -out matrix_GCcont_Mm9_scaledGenes.tab.gz \
 --skipZeros \
 --missingDataAsZero  

$ deepTools-1.5.7/bin/computeMatrix scale-regions \
 -S GCcontent_Dm3_50_5.bw \
 -R Dm530.genes.bed \ 
 -bs 50
 -m 3000 -b 1000 -a 1000 \
 -out matrix_GCcont_Dm3_scaledGenes.tab.gz \
 --skipZeros --missingDataAsZero

$ deepTools-1.5.7/bin/heatmapper \
 -m matrix_GCcont_Dm3_scaledGenes.tab.gz \
 -out hm_GCcont_Dm3_scaledGenes.png \
 --colorMap YlGnBu \
 --regionsLabel 'fly genes' \
 --heatmapHeight 15 \
 --plotTitle 'GC content fly' &

$ deepTools-1.5.7/bin/heatmapper \
 -m matrix_GCcont_Mm9_scaledGenes.tab.gz \
 -out hm_GCcont_Mm9_scaledGenes.png \
 --colorMap YlGnBu \
 --regionsLabel 'mouse genes' \
 --heatmapHeight 15 \
 --plotTitle 'GC content mouse' &

Visualizing CpG methylation around murine transcription start sites in two different cell types

<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	reference-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

The commands for the bigWig files from the ES cell and NP cell sample were the same:

$ deepTools-1.5.7/bin/computeMatrix reference-point \
 -S GSE30202_ES_CpGmeth.bw \
 -R activeGenes_ESConly.bed \
 --referencePoint TSS \
 -a 2000 -b 2000 \
 -out matrix_Genes_ES_CpGmeth.tab.gz

$ deepTools-1.5.7/bin/heatmapper \
 -m matrix_Genes_ES_CpGmeth.tab.gz \
 -out hm_activeESCGenes_CpG_ES_indSort.png \
 --colorMap jet \
 --missingDataColor "#FFF6EB" \
 --heatmapHeight 15 \
 --yMin 0 --yMax 100 \
 --plotTitle 'ES cells' \
 --regionsLabel 'genes active in ESC' 

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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"