Plotting TSS & TTS for Chip-seq peaks

Question

[anu014]

Hello Biostars,

I need a graph showing the distribution of peaks near TSS and transcription termination site (TTS). Can anyone tell me any package/concept for it? I have tried ChIPseeker for TSS plot but I don't know how to plot TTS plot..

Please help me out. Thank you :)

Answer 1

[Simply Bioinformatics]

DeepTools

http://deeptools.readthedocs.io/en/latest/content/example_usage.html

Answer 2

[michael.ante]

Hi Anu014,

You can have a look at the HTSeq case (a TSS tutorial): http://htseq.readthedocs.io/en/release_0.9.1/tss.html It should be easily adaptable for TTS as well.

Cheers,

Michael

Answer 3

[Kristoffer Vitting-Seerup]

Alternative you could just calculate and visualise the distances yourself. The distances can easily be found with GenomicRanges in R.