Transcription of Rsubread/Subread Users Guide
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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. 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 .. 25. 5 Mapping reads generated by RNA sequencing technologies 26.
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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