Question: CIRCOS plot with Chip-Seq Data
2
gravatar for user230613
5.0 years ago by
user230613280
Europe
user230613280 wrote:

Hi all,
I've just finished a chip-seq analysis and I would like to represent the results in a nice way. I was thinking about doing a CIRCOS plot with the peaks detected. I've never work with CIRCOS, and it's my first time with chip-seq data, so I would like to know if anyone have tried to perform a circos with this kind of data, and how the plot looks like. I've read the circos manual from http://circos.ca/documentation/tutorials/, to have a general idea but I would like to focus on chip-seq data. Any help or plot examples would be really appreciated.
I'm planing to use circlize R package.

circos chip-seq • 2.9k views
ADD COMMENTlink modified 9 weeks ago by bernatgel2.6k • written 5.0 years ago by user230613280
0
gravatar for anu014
4.0 years ago by
anu014180
India
anu014180 wrote:

HOMER can also do CIRCOS plot for chip-seq. But it seems it can work only upon Paired-end data. Check it out here : http://homer.salk.edu/homer/interactions/circos.html

ADD COMMENTlink written 4.0 years ago by anu014180
0
gravatar for Andrewoods
2.0 years ago by
Andrewoods100
Andrewoods100 wrote:

Maybe you want to try shinyCircos. It's an interactive APP. https://github.com/venyao/shinyCircos http://shinycircos.ncpgr.cn/

ADD COMMENTlink written 2.0 years ago by Andrewoods100
0
gravatar for bernatgel
9 weeks ago by
bernatgel2.6k
Barcelona, Spain
bernatgel2.6k wrote:

If you would be also happy with non-circular plot, you can try with karyoploteR. It's an R/Bioconductor package and it should be easier to grasp than circos config files.

As Circos, it can represent any data type, including ChIP-seq data and you can zoom in to your regions of interest pretty easily.

This is an example from the karyoploteR tutorial plotting ENCODE data (including ChIP-seq data) around TP53.

Example of karyoploteR plot with ENCODE data arround TP53 gene. It includes ChIP-seq data and other data types.

ADD COMMENTlink written 9 weeks ago by bernatgel2.6k
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