Deeptools correlation plot: between RNAseq and H3K27ac ChIPseq
0
0
Entering edit mode
9 months ago
aditi225 • 0

Hi, I have been trying to plot correlation between my transcriptome and epigenome (H3K27ac) data but it shows almost no correlation. Within transcriptome and epigenome samples, the correlation is fine but I am not sure deeptools is a good way to plot correlation between RNAseq and H3K27ac ChIPseq. Here is my command:

python3 multiBamSummary bins --bamfiles /*R*bam  --smartLabels -o multibam.npz -p 20

python3 plotCorrelation -in multibam.npz --corMethod pearson --skipZeros --whatToPlot scatterplot -o multibam_perason.png   --outFileCorMatrix pearson.tab

Link to images:

RNA-Seq ChIP-Seq deeptools correlation H3K27ac • 348 views
ADD COMMENT
1
Entering edit mode

Presumably you have MANY bins with no signal, have you tried excluding them?

ADD REPLY
0
Entering edit mode

It remains the same even when I used BED files for locus specific correlations. Thanks

ADD REPLY
0
Entering edit mode

You might scroll around with IGV a bit just to eye-ball whether these values seem reasonable. I haven't looked at this particular correlation myself, so I don't really know what to expect. You may also use the --log1p option, which won't change the correlation, but will make the graphs easier to see.

ADD REPLY
1
Entering edit mode

I would recommend to call H3K27ac peaks, get nearest/overlapping genes with bedtools nearest, and plot the peaks maximum value alongside the associated genes expression with R / Python / Excel.

Otherwise, rank genes from the most expressed to the least expressed and make a heatmap with deepTools plotting H3K27ac at these genes TSS (computeMatrix followed by plotHeatmap) while keeping the expression ranked genes order (--sortRegions keep). I did that kind of analysis to validate RNA-seq / FAIRE-seq correlation (noisy old-fashioned open chromatin signal) and it worked like a charm.

ADD REPLY
0
Entering edit mode

Please use these directions: How to add images to a Biostars post

ADD REPLY
0
Entering edit mode

I'll do that, thanks.

ADD REPLY

Login before adding your answer.

Traffic: 2137 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