Question: plotProfile (deepTools) generated a peak on gene body region
0
gravatar for mbk0asis
2.9 years ago by
mbk0asis570
Korea, Republic Of
mbk0asis570 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 • 2.4k views
ADD COMMENTlink modified 5 months ago by Shaurya Jauhari40 • written 2.9 years ago by mbk0asis570

Hello.

Not sure if my problem aligns perfectly to this thread, but I want to share some weird plots from the computeMatrix-plotProfile workflow. Not sure about "flatness" of the plot.

computeMatrix scale-regions \
-R LD9783.bed \
-S H3K4me1.bw \
H3K4me2.bw \
H3K4me3.bw \
H3K27ac.bw \
-p 1 \
-—regionBodyLength 2000 \
-a 1000 -b 1000 \
--samplesLabel "H3K4me1" "H3K4me2" "H3K4me3" "H3K27ac" \
-o A549_LD9783.gz \
--outFileNameMatrix A549_LD9783.tab \
--outFileSortedRegions A549_LD9783.bed

The corresponding plotProfile script is as under.

plotProfile -m A549_LD9783.gz -out A549_LD9783.png --numPlotsPerRow 2 --plotTitle "A549|LD9783"

The plot is very boxy and abrupt. I have checked the bedGraph values and they aren't uniform as such.

enter image description here

Any suggestions on what could be erroneous here.

ADD REPLYlink modified 5 months ago • written 5 months ago by Shaurya Jauhari40

Use the directions: How to add images to a Biostars post

Create a new thread if this is not directly related to the original question.

ADD REPLYlink written 5 months ago by genomax91k
0
gravatar for Devon Ryan
2.9 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k 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 2.9 years ago by Devon Ryan97k

Thank you. I will give it a try.

ADD REPLYlink written 2.9 years ago by mbk0asis570

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 2.9 years ago by mbk0asis570

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 2.9 years ago by Devon Ryan97k

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

ADD REPLYlink written 2.9 years ago by mbk0asis570
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