plotprofile multiple replicates from two groups on a single plot

[christianma...@u.northwestern.edu]

Hi all,

I am using deeptools to obtain profile plots on ChIP-seq data. I have 6 .bw files (basically the classic experiment with 2 groups in triplicates) and a single BED file. I tested computeMatrix and plotprofile with 2 .bw files and I can plot 2 samples (one per group) on a single plot using the --perGroup flag, getting exactly the result I expected.

Is there a way to plot all 6 .bw on a single plot (so by the regions specified in the BED file) and color code them by group? Say blue for one group of triplicates and red for the other group of triplicates. Do I need to change anything in the computeMatrix command? I would just input all .bw files as explained in the documentation:

computeMatrix scale-regions -S ./*.bw -R regions.bed -o Allsamplesmatrix.gz --regionBodyLength 2000 -a 3000 -b 1000

After this though I am not sure how to get everything on one plot color coded. Does anybody have any advice about this?

Thanks a lot for your input!

Christian

[Devon Ryan]

Hi Christian,

You can use plotProfile or plotHeatmap as normal and use the `--perGroup` option to get all profile plots together. You can then manually specify the coloring of each sample with the `--colors`, such as `--colors red red red blue blue blue`.

Devon

--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51

79108 Freiburg

Germany

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