SplAdder-event-calling/README.md

# README.md

> Author: Qingwang Chen
>
> Email: [qwch20@fudan.edu.cn](mailto:qwch20@fudan.edu.cn)
>
> Last Updates: 24/08/2021

#### Brief Introduction

 The the joint graph is fully quantified and we can move on to use it for downstream analyses, for instance to extract different AS events:

--event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip (Pick one at a time for analysis)

#### Requirements

- choppy
- Ali-Cloud
- Linux

```
# 激活choppy环境
$ source activate choppy (open-choppy-env)

# 第一次安装
$ choppy install chenqingwang/SplAdder-event-calling
# 非第一次安装
$ choppy install chenqingwang/SplAdder-event-calling -f 

# 查询已安装APP
$ choppy apps
```

#### Quick Start

```
# 准备 samples.csv 文件
$ choppy samples chenqingwang/SplAdder-event-calling-latest > samples.csv
# 准备无默认参数的samples.csv 文件
$ choppy samples --no-default chenqingwang/SplAdder-event-calling-latest > samples.csv

# 提交任务
$ choppy batch chenqingwang/SplAdder-event-calling-latest samples.csv -p Your_project_name -l Your_label

# 查询任务运行状况
$ choppy query -L Your_label | grep "status"

# 查询失败任务
$ choppy search -s Failed -p Your_project_name -u chenqingwang --short-format

# 结果文件地址
$ oss://choppy-cromwell-result/test-choppy/Your_project_name/
```

#### Description
```
# samples: The file names to be analyzed should be written line by line in this file, and the file should be uploaded to AliCloud.

```