{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Liu D"],"funding":["PTEN Research","NICHD NIH HHS","Cleveland Clinic","Cleveland Clinic Foundation","American Academy of Neurology"],"pagination":["103357"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11489062"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["5(4)"],"pubmed_abstract":["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.<sup>1</sup>."],"journal":["STAR protocols"],"pubmed_title":["Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing."],"pmcid":["PMC11489062"],"funding_grant_id":["R01 HD105049"],"pubmed_authors":["Dhawan A","Ni Y","Liu D","Yehia L","Eng C"],"additional_accession":[]},"is_claimable":false,"name":"Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing.","description":"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.<sup>1</sup>.","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Dec","modification":"2026-07-01T03:16:36.631Z","creation":"2025-04-21T21:46:27.891Z"},"accession":"S-EPMC11489062","cross_references":{"pubmed":["39368093"],"doi":["10.1016/j.xpro.2024.103357"]}}