Rsubread/Subread Users Guide

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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).

The Subindel program carries out local read assembly to discover long insertions and deletions. Read mapping should be performed before running this program. The featureCounts program is designed to assign mapped reads or fragments (paired-end data) to genomic features such as genes, exons and promoters. It is a light-weight read counting 3

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