Metagene for first last and intermediate exons?

Question

[PK]

Hi all,

I was able to do the metagene plot for 5'utr exon and 3' utr. My question is, is there any way to do the metagene plot for first, last and intermediate exons.

[seidel]

You can make a metagene plot for any shared feature among genes. Where are you stuck? What have you tried?

[PK]

Hi, I used following command to produce the metageneplot

cvgs.utr5 <- coverageDepth("bamfilename", gtf = txdb, region="utr5")

and i did for CDS and utr3

metaPlot(cvgs.utr5, cvgs.CDS, cvgs.utr3, sample=1,xaxis = "mRNA")

which produced this plot

But if you look at towards stop there is clear spike which is present in all the KO compare to wild type. Additionally, i did for each files is there any way to combine replicates together?