Transcription of Rsubread/Subread Users Guide - Bioconductor
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Rsubread/Subread Users Guide - Bioconductor
Rsubread/Subread Users GuideRsubread October 2021 Wei Shi and Yang LiaoOlivia Newton-John Cancer Research InstituteMelbourne, AustraliaCopyright 2011 - 2021 Contents1 Introduction32 Citation .. Download and installation .. BioconductorRsubreadpackage .. SourceForgeSubreadpackage .. How to get help ..73 The seed-and-vote mapping Seed-and-vote .. Detection of short indels .. Detection of exon-exon junctions .. Detection of structural variants (SVs) .. Two-scan read alignment .. Multi-mapping reads .. Mapping of paired-end reads ..124 Mapping reads generated by genomic DNA sequencing A quick start for using SourceForgeSubreadpackage .. A quick start for using BioconductorRsubreadpackage .. Index building .. Read mapping .. Memory use and speed .. Mapping quality scores .. Mapping output .. Mapping of long reads ..255 Mapping reads generated by RNA sequencing A quick start for using SourceForgeSubreadpackage.
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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