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YaqingLiu
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README.md
README.md
Author: Yaqing Liu
Email: yaqing.liu@outlook.com
Last Updates: 23/04/2021
Requirements
- choppy
- Ali-Cloud
- Linux
Introduction
This APP is used to
- convert a FASTQ file to an aligned BAM file.
- QC the data at the level of FASTQ and BAM, based on FastQC, FastQ Screen and Qualimap.
Please carefully check the reference genome, bed file, etc.
Usage
open-choppy-env
choppy install YaqingLiu/cbcga-wes-qc-latest
choppy samples YaqingLiu/cbcga-wes-qc-latest --no-default
# sample_id,fastq_1,fastq_2
choppy batch YaqingLiu/cbcga-wes-qc-latest samples.csv -p Project -l Label
# Query the status of all tasks in the project
choppy query -L Label | grep "status"