ChIPseeker-tts plot profile

Question

[ab2063]

I want to plot peaks around tts, just like tss using chipseeker but I am unable to do so. Any suggestions.

[ATpoint]

We cannot read minds, nor see your screen. Please invest effort, show code and describe what the problems are.

[ab2063]

As i understand chipseeker allows plotting density profiles of ChIP peaks only around promoter, exon and intron and not tts. I want to plot around TTS

[ATpoint]

With respect ab2063, either you show effort and clearly explain where the issues are by actually showing data and code, or I am going to close this thread. We are a community driven by volunteers, and as such it is the responsibility of the user to provide adequate information that allows reproduction of the problem. It is not the idea that users first have to ask and inquire what the problems are.

[[ Please read before posting a question ::: How To Ask A Good Question ]]

[ab2063]

I am a beginner in R. And using ChIPseeker package for plotting ChIP peaks around TSS.

promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000) tagMatrix <- getTagMatrix(peak, windows=promoter) plotAvgProf(tagMatrix, xlim=c(-3000, 3000))

Apart from promoter, we can use getBioRegion to define a region center on start site of selected feature which are one of 'gene', 'transcript', 'exon', 'intron'.

I need a graph showing the distribution of peaks near TSS and transcription termination site (TTS), both. I have tried ChIPseeker for TSS plot as shown above but I don't know how to plot TTS plot using ChIPseeker or any other package. I do not know how to put my question in a better way.

Answer 1

[ATpoint]

Thanks for adding details, and sorry for sounding harsh, that was not my intend. You can download a reference annotation in GTF format and then load it into R with e.g. rtracklayer::import(). This will give you a GRanges object which you can then filter for TSS and TTS. This would then be your windows input. TSS would simply be the start of annotated transcripts (or the end if they are on the minus strand), and TTS vice versa, so start coordinate if on the minus strand and end if on the plus strand.

[ab2063]

Thanks so much. I was able to make the plots.

[ATpoint]

Cool!