genotyping_main: Genotype a Crispr Locus

In blaserlab/genotyping.functions: Supplies Functios For Zebrafish Genotyping

Genotype a Crispr Locus

Description

Use this function to genotype a target crispr locus.

Usage

genotyping_main(
  crispr_target,
  genome = c("Drerio", "GFP"),
  network_directory,
  multiplex = TRUE,
  read_threshold = 25,
  bed = "data-raw/master.bed",
  split_snv = TRUE,
  txdb = system.file("extdata/GRCz11.97_txdb.sqlite", package =
    "BSgenome.Drerio.blaserlabgenotyping.dr11"),
  cutadapt_path = "/workspace/python/anaconda3/envs/cutadaptenv/bin/cutadapt"
)

Arguments

crispr_target	The name of the crispr target locus. Must be present on the master BEDfile
genome	The genome to use. Can be either Drerio or GFP. Default is Drerio.
network_directory	Network directory containing fastqs. The fastqs can be nested in a subdirectory; the output will be placed in the directory named.
multiplex	Whether or not to demultiplex, Default: TRUE
read_threshold	Remove alleles with read counts below this threshold, Default: 25
bed	master bedfile to use, Default: 'data-raw/master.bed'
split_snv	If TRUE, will count SNVs as variant alleles.
txdb	transcriptome database to use. If using a nonstandard transgene, should be set to NULL.
cutadapt_path	The path to your cutadapt binary. Find this by running $ which cutadapt in your terminal.

Value

Nothing; writes out to the network directory.

See Also

character(0) detectCores

blaserlab/genotyping.functions documentation built on Oct. 16, 2024, 1:40 a.m.