addInputReadCounts: addInputReadCounts

In ge11232002/NGS: Next Generation Sequencing Data Analysis

Description

Add the number of input reads as a comment to the header of bamFile.

Usage

  addInputReadCounts(bamFiles, reads1s, binary = "samtools")

Arguments

bamFiles	The filenames of input bam files.
reads1s	The filenames of the corresponding input fastq files.
binary	The name/filename of the binary "samtools" to call.

Value

The filenames of input bam files.

Author(s)

Ge Tan

Examples

  
  ## This example is not tested because it requires external software "samtools"
  bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                         mustWork=TRUE)
  tempBamFile <- tempfile(fileext=".bam")
  file.copy(bamfile, tempBamFile)
  reads1 <- file.path(system.file("extdata", package="NGS"), "fastq",
                      "nanocage_ACAGAT_carp_embryo_R1.fastq")
  addInputReadCounts(bamFiles=tempBamFile, reads1s=reads1, binary="samtools")
  file.remove(tempBamFile)
  

ge11232002/NGS documentation built on May 17, 2019, 12:13 a.m.