正式进入cancer genomics领域,只不过是从scRNA-seq与scATAC-seq入手。
我们的问题是如何从有限的SNV和CNV数据里推测出CRC的lineage的关系。
使用的工具:
- https://github.com/single-cell-genetics/MQuad
- https://github.com/single-cell-genetics/cellsnp-lite
这属于单细胞genomics领域,应该是传统计算生物学家研究扎堆的地方,能用好工具就行,不要贸然开发,否则很容易烂尾。
一些想法:
- 多组学call CNV目前还没有很好的工具;
- entropy很鸡肋,能否做个多组学的工具;
- 多组学call variant,用CNV和SNV(genome + MT)来构建clone structure
推测样本内和样本间的关系。
其他参考:
- single-cell in silico lineage tracing
- ATAC-seq variant lineage tracing
- Introducing the Innovator Series: Hacking ATAC-seq to perform clonal lineage tracing in tumors
- Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA
- single cell lineage tree based on SNV
- Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm
- BiTSC2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data
标签:CNV,lineage,SNV,tree,cell,MT,single From: https://www.cnblogs.com/leezx/p/17029388.html