memcrispr.align: Align reads to reference

In grimbough/MEMcrispR: Mixed Effects Model for the analysis of CRISPR screens

Description

This function expects to be provided a folder containing FASTQ files produced by sequencing a genetic screening experiment. It will align the reads against a reference sequence generated from specified guide libraries.

Usage

memcrispr.align(
  path,
  sampleSheet = NULL,
  outputDir = NULL,
  guideLibraries = c("GeCKOv2_A", "GeCKOv2_B"),
  guidePrefix = NULL,
  guideSuffix = NULL,
  ncores = 4
)

Arguments

path	Full file path to the folder containing the data.
sampleSheet	Name of the file specifying the structure of the experiment. If left NULL a default of 'SampleSheet.txt' is used.
outputDir	Full path to the location where output files should be written. If left NULL the current working directory is used.
guideLibraries	Names of libraries to align against. These can be paths to files for custom libraries not included in the package.
guidePrefix	Depending upon the CRISPR library you are using you may expect all your reads to contain a common sequence before (5' of) the particular guide is read. Provide this common sequence here to aid with alignment.
guideSuffix	Similar to guidePrefix, but for a common sequence that appears after (3' of) the guide sequence.
ncores	The number of CPU cores to be used by the Rsubread aligner. Defaults to 4.

grimbough/MEMcrispR documentation built on Feb. 4, 2021, 5:26 a.m.