rnaseq-engineering/README.md

Author: Jun Shang

Email: shangjunv@163.com

Last Updates: 29/06/2020

Requirements

• choppy
• Ali-Cloud

$ source activate choppy/open-choppy-env
$ choppy install junshang/rnaseq-engineering:tag
$ choppy apps

quick start

$ choppy samples junshang/rnaseq-engineering-latest > samples.csv
$ choppy batch junshang/rnaseq-engineering-latest samples.csv -p Your_project_name

The samplec.csv looks like this: | sample_id | disk_size | read1 | read2 | pre_alignment_qc | qualimap_qc | trim_adapter | | --------- | --------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------- | ----------- | ------------ | | FDU_D5 | 200 | oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R1_400k.gz | oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R2_400k.gz | false | true | true |

• sample_id 一般设置为文件输出前缀
• read1 R1 fastq 文件所在路径
• read2 R2 fastq 文件所在路径
• disk_size 磁盘空间，每一步中间文件大小做调整
• pre_alignment_qc: 执行 fastqc 和 fastq screen 设置为 true，反之设置为 false
• qualimap_qc: 执行 qualimap bamqc 设置为 true，反之设置为 false
• trim_adapter: 使用 fastp 去 adapter 设置为 true，反之设置为 false

参考文献

APP 主要来自于 Quartet RNA-seq 标准流程