Question

Plotting TSS & TTS for Chip-seq peaks

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6.5 years ago

anu014 ▴ 190

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 :)

ChIP-Seq plot next-gen • 5.8k views

ADD COMMENT • link updated 6.4 years ago by Simply Bioinformatics ▴ 200 • written 6.5 years ago by anu014 ▴ 190

score 4 · Answer 1 · 2017-11-09

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6.4 years ago

Simply Bioinformatics ▴ 200

DeepTools

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

ADD COMMENT • link 6.4 years ago by Simply Bioinformatics ▴ 200

score 1 · Answer 2 · 2017-10-27

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6.5 years ago

michael.ante ★ 3.8k

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

ADD COMMENT • link 6.5 years ago by michael.ante ★ 3.8k

score 0 · Answer 3 · 2017-10-27

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6.5 years ago

Kristoffer Vitting-Seerup ★ 4.0k

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

ADD COMMENT • link 6.5 years ago by Kristoffer Vitting-Seerup ★ 4.0k