Question: plotProfile (deepTools) generated a peak on gene body region
0
gravatar for mbk0asis
17 months ago by
mbk0asis410
Korea, Republic Of
mbk0asis410 wrote:

Hi, all!

I'm trying to plot the DNA methylation profiles using deepTools and having annoying peaks on the gene body region as you can see the picture below.

enter image description here

The code I used;

$ computeMatrix scale-regions -S Sample1.bw Sample2.bw Sample3.bw -R genes.bed -a 5000 -b 5000 -o Samples.matrix --regionBodyLength 15000 --skipZeros
$ plotProfile -m Samples.matrix -out Samples.profile.png --perGroup

How can I remove them?

Thank you!

deeptools plotprofile • 1.3k views
ADD COMMENTlink modified 17 months ago by Devon Ryan90k • written 17 months ago by mbk0asis410
0
gravatar for Devon Ryan
17 months ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

Give plotHeatmap a try, I expect you have some outlier bin in one gene (just remove that gene, though in the future you'll want to blacklist that region when making bigWig files) that will be apparent in the heatmap.

ADD COMMENTlink written 17 months ago by Devon Ryan90k

Thank you. I will give it a try.

ADD REPLYlink written 17 months ago by mbk0asis410

I am stuck at the first step which is ID the outliers. I was going to export the matrix using "–outFileNameMatrix" option and edit the matrix. Then, how can I make the edited file back to the matrix file 'plotHeamap' recognizes? Should I just use other tools like R to draw the heatmap?

ADD REPLYlink written 17 months ago by mbk0asis410

If you want to actually edit the heatmap then don't bother with --outFileNameMatrix, just gunzip the output from computeMatrix, remove the problematic line, change the group_boundaries so they limits are correct, and then gzip the results back up.

In general, it's probably simpler to just figure out where the problem region is and remake the bigWig files with that region blacklisted.

ADD REPLYlink written 17 months ago by Devon Ryan90k

Your second suggestion sounds much easier, haha. Thank you!

ADD REPLYlink written 17 months ago by mbk0asis410
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