RNA Sequencing Alignment Pipeline

Author: Li Zhihuil; Qingwang Chen

E-mail：qwchen20@fudan.edu.cn

Git: http://choppy.3steps.cn/renluyao/RNAseq_germline_datapotal.git

Last Updates: 2020/12/02

Brief Introduction For RNA-seq data, from bams to AS Information files.

Requirements choppy Ali-Cloud Linux

激活choppy环境

$ source activate choppy (open-choppy-env)

第一次安装

$ choppy install chenqingwang/RNAseq-alignment

非第一次安装

$ choppy install chenqingwang/RNAseq-alignment -f

查询已安装APP

$ choppy apps Quick Start

准备 samples.csv 文件

$ choppy samples chenqingwang/RNAseq-alignment-latest > samples.csv

准备无默认参数的samples.csv 文件

choppy samples --no-default chenqingwang/RNAseq-alignment-latest > samples.csv

提交任务

$ choppy batch chenqingwang/RNAseq-alignment-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/