rMATS-ISO Code
rMATS-Iso is a generalization of rMATS for complex splicing patterns.
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Getting started with toy example in
Tree [fbd167] master / History
| File | Date | Author | Commit |
|---|---|---|---|
| ISOClassify | 2018-05-30 |
Shihao Shen
|
[db2e24] first |
| ISOPlot | 2018-05-30 |
shihaoshen
|
[e6f65f] Update README.md |
| IsoModule | 2018-06-06 |
Yan Gao
|
[ddb2e9] add PC3E-GS689 test data |
| lr2rmats | 2018-06-06 |
Yan Gao
|
[ddb2e9] add PC3E-GS689 test data |
| rmats-EM | 2018-05-30 |
Shihao Shen
|
[db2e24] first |
| test_data | 2018-06-06 |
Yan Gao
|
[ddb2e9] add PC3E-GS689 test data |
| .gitignore | 2018-06-06 |
Yan Gao
|
[ddb2e9] add PC3E-GS689 test data |
| Fig1_Diagram-01.jpg | 2018-05-30 |
shihaoshen
|
[05eed0] Add files via upload |
| LICENSE | 2018-05-30 |
Shihao Shen
|
[db2e24] first |
| Makefile | 2018-05-30 |
Shihao Shen
|
[db2e24] first |
| README.md | 2018-06-06 |
shihaoshen
|
[fbd167] Update README.md |
| long_read_fa_input.list.example | 2018-05-30 |
Shihao Shen
|
[db2e24] first |
| rMATS-ISO.py | 2018-06-06 |
Yan Gao
|
[ddb2e9] add PC3E-GS689 test data |
| short_read_bam_input.list.example | 2018-05-30 |
Shihao Shen
|
[db2e24] first |
| short_read_fa_input.list.example | 2018-05-30 |
Shihao Shen
|
[db2e24] first |
| utils.py | 2018-05-30 |
Shihao Shen
|
[db2e24] first |
Read Me
rMATS-ISO
What is rMATS-ISO ?
rMATS-Iso is a generalization of the rMATS statistical framework, and the first event-based tool which can detect differential AS in splicing modules with complex splicing patterns using replicate RNA-seq data. The rMATS-Iso statistical model utilizes a hierarchical framework to account for both the estimation uncertainty in PSI values in individual replicates as well as the variation among replicates.
Table of Contents
- What is rMATS-ISO ?
- Installation
- Operating system
- Cloning and building rMATS-ISO pipeline
- Components
- Getting started with toy example in
test_data - Output folder
- Contact
Installation
Operating system
rMATS-ISO currently can only be built and run on Linux/Unix systems.
Cloning and building rMATS-ISO pipeline
git clone https://github.com/Xinglab/rMATS-ISO.git --recursive
cd rMATS-ISO
make
export PATH=$PATH:$PWD/lr2rmats/bin # To permanently modify your PATH, you need to add it to your ~/.profile or ~/.bashrc file.
After the building is done, the path of rMATS-ISO/lr2rmats/bin needs to be added to the environment variable PATH.
Components
rMATS-ISO consists of following components: lr2rmats, IsoModule and rMATS-EM.
They will all be automatically downloaded and built via make command.
Getting started with toy example in test_data
python ./rMATS-ISO.py --in-gtf ./test_data/gtf/PC3E_GS689.gtf --in-bam ./test_data/PC3E_GS689_short_read_bam_input.list -o ./output2/
All the output files and intermediate files will be generated in ./output folder.
Output folder
Usually the output folder will contain these following sub-folders:
EM_out/
ISO_classify/
ISO_module/
ISO_plot/
lr2rmats/
STAR_mapping/
Contact
Yi Xing yxing@ucla.edu
