Deeptools heatmap analysis - graphing unique clusters of heatmap
1
2
Entering edit mode
16 months ago
jamzaleg84 ▴ 50

Hello,

I used deeptools to make a heatmap of a ChIP-seq experiment with 4 samples - WT_TF1, WT_TF2, Mutant_TF1, and Mutant TF2. I made the heatmap referenced to a bedfile of all unique peak sites for all the conditions. I used the --kmeans option of plotHeatmap in an attempt to do a clustering analysis whereby the clusters note enrichment of binding in some samples but not all (For example, cluster 1 could show regions where all samples bind, cluster 2 shows regions where sample 1 and 2 bind but not sample 3, etc). I wanted to know if there was a way of graphing the different clusters similar to the way it was done in Miranda et al (the figure on the right side). Attached below a picture of my heatmap generated from plotHeatmap and a picture of what was done in the Miranda paper. The Miranda paper used Homer to do the ChIP-seq analysis and it wasn't so clear ho they made the graph next to the heatmap. I was wondering if anyone knew of a way I could generate the graph with my data. enter image description here enter image description here

Thank you so much,

deeptools plotHeatmap computeMatrix • 841 views
ADD COMMENT
1
Entering edit mode
16 months ago

The graph to the right is what you get from plotProfile.

ADD COMMENT

Login before adding your answer.

Traffic: 2125 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6