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Rsubread/Subread Users Guide

Rsubread/Subread Users Guide Rsubread 14 July 2021. Wei Shi and Yang Liao Olivia Newton-John Cancer Research Institute Melbourne, Australia Copyright 2011 - 2021. Contents 1 Introduction 3. 2 Preliminaries 5. Citation .. 5. Download and installation .. 6. Install Bioconductor Rsubread package .. 6. Install SourceForge Subread package .. 6. How to get help .. 7. 3 The seed-and-vote mapping paradigm 8. Seed-and-vote .. 8. Detection of short indels .. 9. Detection of exon-exon junctions .. 10. Detection of structural variants (SVs) .. 11. Two-scan read alignment .. 12. Multi-mapping reads .. 12. Mapping of paired-end reads .. 12. 4 Mapping reads generated by genomic DNA sequencing technologies 14.

featureCounts read quanti cation program, exactSNP SNP calling program and other utility programs. This document provides a detailed description to the programs included in the packages. Subread and Subjunc aligners adopt a mapping paradigm called \seed-and-vote" [1]. This is an elegantly simple multi-seed strategy for mapping reads to a ...

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