mapToBarcodes: Map case and control fastq files to unique oligo barcodes and...

In cshukla/oligoGames: Analyze data from massively parallel reporter assays

Description

This function allows you to map your sequencing files back to the oligo pool and compile a table describing counts for each oligo. For a read to map to an oligo, 2 conditions must be satisfied: (1) The first 10 nucleotides of the read should perfectly map one barcode in the pool and (2) The remaining nucleotides should have no more than 2 mismatches to the variable sequence linked with the barcode.

Usage

mapToBarcodes(fastqCases, fastqControls, conditionLabels = c("case",
  "control"), oligoMap = "oligoMap.fa", oligoOut = "oligoOut")

Arguments

fastqCases	character vector with the name of 'case' fastq files.
fastqControls	character vector with the name of 'control' fastq files.
conditionLabels	character vector of length two which contains the condition labels for the two conditions that are being compared. Default value is c("case", "control")
oligoMap	the name of the tab seperated file which provides a link between oligo name, barcode and variable sequence. The file should have columns for the name, barcode sequence and variable sequence of the oligo.
oligoOut	the name of the directory where the output file will be written. If the output directory does not exist, one will be created. Defaults to oligoOut

cshukla/oligoGames documentation built on May 27, 2019, 8:44 a.m.