count_reads: Counting reads across intervals
In seqbias: Estimation of per-position bias in high-throughput sequencing data

Description Usage Arguments Details Value Note Author(s) See Also Examples

Counts the number of reads starting at each position across given genomic intervals

1	count.reads(reads_fn, I, sb=NULL, binary=FALSE, sum.counts=FALSE)

`reads_fn`	filename of aligned reads in BAM format
`I`	a GRanges object giving valid genomic intervals
`sb`	a seqbias object
`binary`	if `TRUE`, return a 0-1 vector, otherwise return a vector counting the number of reads mapped to each position
`sum.counts`	if `TRUE` return the total read count for each interval

Given an indexed BAM file, this function counts the number of reads starting at each position of each provided interval. If a seqbias object is provided through the sb attribute, counts are corrected for sequence bias. The total read count for each interval is returned if sum.counts is TRUE.

If binary is TRUE a 0-1 vector is returned instead, where positions at which no reads are mapped are 0, and those with one or more are 1.

A list of numeric vectors is returned, one for each interval provided. Each vector gives an integer count of the number of reads beginning on that position.

The BAM file provided should be indexed with 'samtools index'.

Daniel Jones dcjones@cs.washington.edu

seqbias.predict

  reads_fn <- system.file( "extra/example.bam", package = "seqbias" )

  I <- GRanges( c('seq1'), IRanges( c(1), c(5000) ), strand = c('-') )

  counts <- count.reads( reads_fn, I )