symlink.fastqs: Symlink Fastqs

In kstagaman/sharpton-lab-dada2-pipeline: Provides Functions to Easily Replicate the Sharpton Lab dada2 Pipeline

Symlink Fastqs

Description

A function to create symlinks with easier to parse names that the typical names that files have coming off the sequencing machine

Usage

symlink.fastqs(
  seq.dirs,
  ids.tbl,
  smpl.id.col = "Sample",
  file.id.col = 2,
  run.id.col = NULL,
  split.pattern = "--",
  quiet = FALSE
)

Arguments

seq.dirs	The path(s) to the directory(s) in which the raw sequence files are contained. If there are multiple paths, this needs to be a named vector that is reflected in the ids.tbl provided as well.
ids.tbl	A data.frame or data.table containing sample names in one column and their corresponding file IDs in another (e.g. barcodes or sample IDs as used in the raw sequence files). Sample names and file IDs *may* be identical in some instances, please still provide a two column table.
smpl.id.col	The name/number of the column in the ‘ids.tbl' that contains the name of the samples, which will be used in naming the symlinks. Default is ’Sample'.
file.id.col	The name/number of the column in the 'ids.tbl' that contains the corresponding file IDs for matching raw sequence files. Default is 2.
split.pattern	A character string containg the pattern you want to use to separate the sample name and R1/R2 in the symlink names. Default is '–'.
quiet	Logical, if TRUE, there will be no printing of progress. Default is FALSE

kstagaman/sharpton-lab-dada2-pipeline documentation built on Sept. 24, 2022, 11:41 a.m.