Darren Liu, Lamis Yehia, Andrew Dhawan, Ying Ni, Charis Eng
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引用次数: 0
摘要
循环无细胞DNA（cfDNA）片段末端主题图谱是精准肿瘤学中一种很有前景的生物标记物。在这里，我们介绍了一种从超低通量全基因组测序（WGS）数据中分析血浆 cfDNA 片段末端主题的方案。我们详细介绍了一个由连续的 bash 脚本组成的管道，用于处理对齐后的 BAM 文件。随后，我们概述了在 R 中对 4-mer 和其他 n-mer cfDNA 片段末端结构进行下游分析和可视化的过程。有关本方案使用和执行的完整细节，请参阅 Liu 等人的文章1。
Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing.
Circulating cell-free DNA (cfDNA) fragment end motif profiles are a promising biomarker in precision oncology. Here, we present a protocol for analyzing plasma cfDNA fragment end motifs from ultra-low-pass whole-genome sequencing (WGS) data. We detail a pipeline composed of sequential bash scripts for processing post-alignment BAM files. Subsequently, we outline the procedure for downstream analysis and visualization of 4-mer as well as other n-mer cfDNA end motifs in R. For complete details on the use and execution of this protocol, please refer to Liu et al.1.
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