Question: Plotting TSS & TTS for Chip-seq peaks
0
gravatar for anu014
3.0 years ago by
anu014180
India
anu014180 wrote:

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 :)

plot chip-seq next-gen • 3.1k views
ADD COMMENTlink modified 3.0 years ago by Simply Bioinformatics170 • written 3.0 years ago by anu014180
4
gravatar for Simply Bioinformatics
3.0 years ago by
WashingtonDC
Simply Bioinformatics170 wrote:

DeepTools

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

ADD COMMENTlink written 3.0 years ago by Simply Bioinformatics170
1
gravatar for michael.ante
3.0 years ago by
michael.ante3.6k
Austria/Vienna
michael.ante3.6k wrote:

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 COMMENTlink written 3.0 years ago by michael.ante3.6k
0
gravatar for kristoffer.vittingseerup
3.0 years ago by
European Union
kristoffer.vittingseerup3.4k wrote:

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

ADD COMMENTlink written 3.0 years ago by kristoffer.vittingseerup3.4k
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