bt.genomecov: Compute the coverage of a feature file among a genome.

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Compute the coverage of a feature file among a genome.

Description

Compute the coverage of a feature file among a genome.

Usage

bt.genomecov(
  i,
  g,
  ibam = NULL,
  d = NULL,
  dz = NULL,
  bg = NULL,
  bga = NULL,
  split = NULL,
  ignoreD = NULL,
  strand = NULL,
  pc = NULL,
  fs = NULL,
  du = NULL,
  five = NULL,
  three = NULL,
  max = NULL,
  scale = NULL,
  trackline = NULL,
  trackopts = NULL,
  output = NULL
)

Arguments

i	<bed/gff/vcf>
g	<genome>
ibam	The input file is in BAM format. Note: BAM _must_ be sorted by position
d	Report the depth at each genome position (with one-based coordinates). Default behavior is to report a histogram.
dz	Report the depth at each genome position (with zero-based coordinates). Reports only non-zero positions. Default behavior is to report a histogram.
bg	Report depth in BedGraph format. For details, see: genome.ucsc.edu/goldenPath/help/bedgraph.html
bga	Report depth in BedGraph format, as above (-bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: "grep -w 0$" to the output.
split	Treat "split" BAM or BED12 entries as distinct BED intervals. when computing coverage. For BAM files, this uses the CIGAR "N" and "D" operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12).
ignoreD	Ignore local deletions (CIGAR "D" operations) in BAM entries when computing coverage.
strand	Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6). - (STRING): can be + or -
pc	Calculate coverage of pair-end fragments. Works for BAM files only
fs	Force to use provided fragment size instead of read length Works for BAM files only
du	Change strand af the mate read (so both reads from the same strand) useful for strand specific Works for BAM files only
five	Calculate coverage of 5" positions (instead of entire interval).
three	Calculate coverage of 3" positions (instead of entire interval).
max	Combine all positions with a depth >= max into a single bin in the histogram. Irrelevant for -d and -bedGraph - (INTEGER)
scale	Scale the coverage by a constant factor. Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). - Default is 1.0; i.e., unscaled. - (FLOAT)
trackline	Adds a UCSC/Genome-Browser track line definition in the first line of the output. - See here for more details about track line definition: http://genome.ucsc.edu/goldenPath/help/bedgraph.html - NOTE: When adding a trackline definition, the output BedGraph can be easily uploaded to the Genome Browser as a custom track, BUT CAN NOT be converted into a BigWig file (w/o removing the first line).
trackopts	Writes additional track line definition parameters in the first line. - Example: -trackopts 'name="My Track" visibility=2 color=255,30,30' Note the use of single-quotes if you have spaces in your parameters. - (TEXT)
output	Output filepath instead of returning output in R.

PhanstielLab/bedtoolsr documentation built on Aug. 29, 2024, 5:37 p.m.