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. A quick start for using SourceForge Subread package .. 14. A quick start for using Bioconductor Rsubread package .. 15. Index building .. 15. Read mapping .. 17. Memory use and speed .. 24. Mapping quality scores .. 24. Mapping output .. 24. Mapping of long reads.

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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