wisekh6/chia-view

20191127

ChIA-view v1.0

--coding by Simon Zhongyuan Tian

• Demo ChIA-view online: https://chia-view.shinyapps.io/ChIA-view-master/.

----a novel visualization pipeline for multiplex chromatin interactions

Simon Zhongyuan Tian, Daniel Capurso, Minji Kim, Byoungkoo Lee, Meizhen Zheng, Yijun Ruan

Recently, we developed ChIA-Drop¹, a novel experimental method for detecting multiplex chromatin interactions with single-molecule precision via droplet-based and barcode-linked sequencing. ChIA-DropBox² a novel toolkit for analyzing and visulizing multiplex chromatin interactions, which includes: a ChIA-DropBox data processing pipeline³ and a visulizing tool ChIA-View⁴.

¹ Meizhen Zheng, Simon Zhongyuan Tian, Daniel Capurso, Minji Kim, Rahul Maurya, Byoungkoo Lee, Emaly Piecuch et al. "Multiplex chromatin interactions with single-molecule precision." Nature 566, 558 (2019). & GSE109355

² Simon Zhongyuan Tian, Daniel Capurso, Minji Kim, Byoungkoo Lee, Meizhen Zheng, Yijun Ruan. "ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions." Nature 566, 558 (2019).

³ https://github.com/TheJacksonLaboratory/ChIA-DropBox.git

⁴ https://github.com/TheJacksonLaboratory/ChIA-view.git

1. ChIA-view Working Enviroment:

• R (v3.5.2)
• RStudio (v1.1.456 )

2. ChIA-view Required R packages

ChIA-View needs many R packages, which will be automaticlly installed at the first run:

bindrcpp (v0.2.2), gggenes (v0.3.2), data.table (v1.11.8), plotly (v4.8.0), xtable (v1.8-3), rgdal (v1.3-6), sp (v1.3-1), leaflet (v2.0.2), shinyWidgets (v0.4.4), shinyjs (v1.0.1.9004), shinydashboard (v0.7.1), colourpicker (v1.0.2), tidyr (v0.8.2), stringr (v1.3.1), sitools (v1.4), cowplot (v0.9.4), ggrepel (v0.8.0), ggforce (v0.1.3), bedr (v1.0.4), pheatmap (v1.0.12), dplyr (v0.7.8), gridExtra (v2.3), reshape2 (v1.4.3), ggplot2 (v3.1.0), RColorBrewer (v1.1-2), shiny (v1.2.0)

3. Execute ChIA-view

By typing following code in RStudio on your computer, you can easily run ChIA-view.

if (!require("shiny")) install.packages("shiny")
runGitHub("ChIA-view_v1.0", "TheJacksonLaboratory")

Or you can download ChIA-View to your local machine from github and run in RStudio.

git clone https://github.com/TheJacksonLaboratory/ChIA-view.git

When we first time run this server, it may cause a little bit longer time to install necessary packages.

4. ChIA-view

• For ChAI-Drop data, only Cluster VIew and Fragment View are avaiable.
• For RNAPII ChIA-Drop data, Cluster VIew, Fragment View, PE VIew and Extrusion View are all aviable.

5. Parameter Adjust

1. Click Update button each time, after you adjusted all/any parameters.

2. Type in folder name of the data you want to upload in "Data Upload/input file" widget.

• e.g. ChIA-Drop Demo data: type in "Demo_chiadrop"

• e.g. RNAP2 ChIA-Drop Demo data: type in "Demo_p2chiadrop"

6. Input data format

* .region --- Input file for ChIA-Drop data visulized in Cluster view and Fragment view,in which one line represents one fragment; fragments are of a same complex owning same GEMID. One of the standard output of ChIA-DropBox data processing pipeline.

Chrom	Start	End	Frag_num/GEM	GEM_ID
chrX	16274973	16275587	2	SHG0055H-1000-10000046-AAACACCAGTAACGATBX1-M02838-FA-1-0

* .region.PEanno --- Input file for RNAP2-ChIA-Drop data visulized in Promoter view and Gene body view, with annotation of fragments by promoter or non-promoter. One of the standard output of ChIA-DropBox data processing pipeline.

Chrom	Start	End	Frag_num/GEM	GEM_ID	PEanno
chrX	16274973	16275587	2	SHG0055H-1000-10000046-AAACACCAGTAACGATBX1-M02838-FA-1-0	P
chrX	16285880	16286464	2	SHG0055H-1000-10000046-AAACACCAGTAACGATBX1-M02838-FA-1-0	E

7. Create input file

We supply a tool (create_input.R) to divide .region or .region.PEanno file from ChIA-DrpBox data processing pipeline to chromosomes specific sub-sets for ChIA-view inputing.

1. Copy .region or .region.PEanno file to ChIA-view folder
2. Open create_input.R in RStudio
3. Modify input file name and output folder name.

   IN="Sample.region"
   OUT="Sample_SUBRGN"

4. Then run it
5. After a while you could find a folder named Sample_SUBRGN, and using this name for ChIA-view input.

  Sample_SUBRGN/
  - chr2L.SUBRDS
  - chr2R.SUBRDS
  - chr3L.SUBRDS
  - chr3R.SUBRDS
  - chr4.SUBRDS
  - chrX.SUBRDS

8 ChIA-view Demo Video