Subread sequence alignment for R

Documentation for package ‘Rsubread’ version 1.22.1

align	Read mapping for genomic DNA-seq and RNA-seq data via seed-and-vote (Subread and Subjunc)
atgcContent	Calculate percentages of nucletodies A, T, G and C in a sequencing read datafile
buildindex	Build index for a reference genome
createAnnotationFile	Create an annotation file from a GRanges object, suitable for featureCounts()
detectionCall	Determine detection p values for each gene in an RNA-seq dataset
detectionCallAnnotation	Generate annotation data used for calculating detection p values
exactSNP	exactSNP - an accurate and efficient SNP caller
featureCounts	featureCounts: a general-purpose read summarization function
findCommonVariants	Finding the common variants among all input VCF files
getInBuiltAnnotation	Retrieve in-built annotations provided by featureCounts function
processExons	Obtain chromosomal coordiates of each exon using NCBI annotation
propmapped	Calculate the proportion of mapped reads/fragments in SAM/BAM files
qualityScores	Extract quality score data in a sequencing read dataset
removeDupReads	Remove sequencing reads which are mapped to identical locations
repair	Re-order paired-end reads to place reads from the same pair next to each other
RsubreadUsersGuide	View Rsubread Users Guide
sam2bed	Convert a SAM format file to a BED format file
subjunc	Read mapping for genomic DNA-seq and RNA-seq data via seed-and-vote (Subread and Subjunc)
write.Rsubread	Create an annotation file from a GRanges object, suitable for featureCounts()