featureCounts_run: Read counts from BAM or SAM files
In e-myers/rnaseq: Process, Analyze and Visualize RNA-seq Data

Description Usage Arguments Details Author(s)

Get raw counts of reads mapped to specified genomic features using featureCount tool from the subread package.

featureCounts_run(inFiles, annotFile,
  fcPath = "/opt/subread-1.6.0-MacOSX-x86_64/bin/", outDest = "./",
  outSuffix = "", runThreadN = 1, pairedEnd = FALSE,
  isStrandSpecific = FALSE, annotFormat = "GTF", multimappers = FALSE,
  dispToText = FALSE)

`inFiles`	Character - BAM or SAM file list
`annotFile`	String - Name (with path) of gtf file with annotations to define features
`fcPath`	String - Path to directory with featureCounts executable
`outDest`	String - Directory where output files should be saved
`outSuffix`	String - will be appended to original filename (and followed by "_fcounts.txt")
`runThreadN`	Numeric - How many cores to use
`pairedEnd`	Logical - Whether data is paired-end
`isStrandSpecific`	Logical - Strand-specific counting (reads will only be counted if they match the strand of the feature)
`annotFormat`	String - "GTF" or "SAF". Format of annotation file.
`multimappers`	Logical - Whether to count multi-mapping reads. All reported alignments will be counted, using the 'NH' tag in the BAMs/SAMs.
`dispToText`	Logical - Whether to send messages that featureCounts normally displays to the screen, to a text file instead

Take a list of SAM or BAM files, and get counts of reads mapped to genomic features in specified annotations file. Command issued will be written to a text file, particularly so you can confirm the annotation file used (unless its filename gets changed). TIME: 1-3m per BAM. Paired-end data is significantly longer. 3-9m on small RNA data when features are ATAC peaks, so probably longer for larger files when features are all exons or all introns Example at the command line (if you want to play with the parameters while looking at just one file, this might be easiest): annotFile=/Volumes/CodingClub1/RNAseq/Metadata/mm10_refGene.gtf # for intronic read counts, use mm10_refSeq_introns_geneids.gtf featureCounts -a $annotFile -o $outputFile $inputFile -T 8

Emma Myers

e-myers/rnaseq documentation built on May 20, 2019, 9:14 p.m.