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).

from each read, called subreads. Instead of trying to pick the best seed, the strategy allows all the seeds to vote on the optimal location for the read. The algorithm then uses more conventional alignment algorithms to ll in detailed mismatch and indel information between the subreads that make up the winning voting block.

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