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fa_first_qc/README.md

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  1. # 原始数据和比对数据的质量控制

  2. 

  3. > Author：Shang Jun

  4. >

  5. > Email: shangjunv@163.com

  6. >

  7. > Date: 2020/12/15

  8. 

  9. # APP 概述

  10. 

  11. 本 APP 包含了原始数据质量控制软件 FastQC 和 FastqScreen 和比对质量控制软件 Qualimap

  12. 

  13. ```bash

  14. # 1. 启动choppy

  15. open-choppy-env

  16. # 2. 安装APP

  17. choppy install junshang/fa_first_qc

  18. # 3. 获得choppy samples的csv文件

  19. choppy samples fa_first_qc-latest --output qc_samples

  20. # 4. 编辑samples文件

  21. # samples_id,inputSamplesFile

  22. # samples_id是choppy对workflow的编号，写阿拉伯数字就行

  23. # 即

  24. # 1,inputSamplesFile的阿里云地址

  25. # 5. 提交任务

  26. choppy batch fa_first_qc-latest --project-name <project_name>

  27. # 6. 查询任务

  28. choppy query -s <workflow_id>

  29. choppy query -s <workflow_id> -m

  30. ```