Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?

Question

[s.singh]

Hi,

I am trying to use "plotAvgProf2" from the ChIPseeker R package. Is it possible to generate the same plot that shows peak bindings with respect to transcription START SITE and STOP SITE both?

This is the current command I am using:

plotAvgProf2(peak1[], TxDb=txdb, upstream=3000, downstream=3000,
           xlab="Genomic Region (5'->3')", ylab = "Read Count Frequency", resample = 1000)

Thanks -S

[Carlo Yague]

Do you want a continous metagene (with gene the distance between TSS and TES scaled so all genes have virtually the same length ? Like this:

Or a discontinuous one where the gene length is not distorted, but the average profiles are interrupted in the middle ? like these:

[s.singh]

yes!!! I have called the peaks using MACS2 and now I want to visualize the ChIP peaks with respect to the transcription start site and transcription stop site....

[Carlo Yague]

Which one is it ? You just answered a "... OR ..." question with "yes" ^^

[s.singh]

so sorry! I want the first one... a continuous metagene (with gene the distance between TSS and TES scaled so all genes have virtually the same length.

BUT I am also interested in learning about the second plot...It seems interesting... how to generate a discontinuous one where the gene length is not distorted, but the average profiles are interrupted in the middle?

[Carlo Yague]

Ok, so as far as I know, I don't think either plot can be made directly in ChIPSeeker. However, TSS-TES metagenes are implemented in many tools, including the R package ngsplot (-R genebody option), or the well docmented deeptools (computeMatrix scale-regions subcommand).

For the discontinuous metagenes, I'm not aware of a tool that would do it automatically, but it is certainly possible to calculate two matrixes (one for centered on TSS, the orther on TES) and merge them manually.