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| @@ -22,6 +22,19 @@ $ choppy samples junshang/rnaseq-engineering-latest > samples.csv | |||
| $ choppy batch junshang/rnaseq-engineering-latest samples.csv -p Your_project_name | |||
| ``` | |||
| | sample_id | disk_size | read1 | read2 | pre_alignment_qc | qualimap_qc | trim_adapter | | |||
| 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 | | |||
| | 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 | |||
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