vartrix | Single-Cell Genotyping Tool

• module: QC
• toolname: doublets
• interpreter: python3
• program: doublets.py

This script is for detect doublets from cellranger single cell gene expression raw matrix of one sample

脚本仓库

https://github.com/anno-sc/doublets

依赖的包

依赖以下python包

1. scrublet
2. DoubletDetection

安装scrublet时遇到cannot import name '_validate_lenghs'的解决办法：numpy兼容性报错修复

调用的方法/包

1. scrublet: https://github.com/AllonKleinLab/scrublet
2. DoubletDetection: https://github.com/JonathanShor/DoubletDetection
3. scrublet and DoubletDetection

   方法介绍

• https://mp.weixin.qq.com/s/XfrvPEzANuuHFlLv34c5nA
• https://mp.weixin.qq.com/s/b9NiL5NdiG5QMret5m-RXw

usage

参数介绍

• -i : inDir, one sample matrix.mtx, barcodes.tsv, genes.tsv files in the dir
• -o : output dir
• -s : output file prefix
• -m : select method to detect doublets, default scrublet_doubletdetection
• -edr : scrublet.Scrublet expected_doublet_rate, 采用程序默认值即可
• -sdr : scrublet.Scrublet sim_doublet_ratio, 采用程序默认值即可

通过tools调用

/path/tools QC doublets -i /path/sampledir -s sample1 -o /path/outDir

直接使用程序

python3 doublets.py -i /path/sampledir -s sample1 -o /path/outDir

输出介绍

• sample1_doubletdetection_UMAP.pdf
• sample1_doubletdetection_convergence.pdf
• sample1_doubletdetection_threshold.pdf
• sample1_scrublet_UMAP.pdf
• sample1_scrublet_doublet_score_histogram.pdf
• sample1_scrublet_doubletdetection_doublets_ratio.csv

  双细胞比例统计，csv格式

• sample1_scrublet_doubletdetection_mark_doublets_barcodes.csv

  两种算法标记的每个barcode是否双细胞，csv格式

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