cutadapt: Function to execute Cutadapt on RNA-Seq reads

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Function to execute Cutadapt on RNA-Seq reads

Description

This function executes the docker container by running CutAdapt algorithm a the input RNA-Seq dataset to remove the sequencing adapters.

Usage

cutadapt(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  adapter.type = c("NEB", "ILLUMINA", "QIAGEN", "LEXOGEN", "DIAGENE", "SEQMATIC",
    "TRILINK"),
  threads = 1
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
scratch.folder	a character string indicating the scratch folder where docker container will be mounted
data.folder	a character string indicating where fastq files are located
adapter.type	a character string. Seven options are available depending on which miRNA library prep was used: NEB, ILLUMINA, QIAGEN, LEXOGEN, DIAGENE, SEQMATIC, TRILINK
threads	a number indicating the number of cores to be used from the application

Value

The fastq files of the trimmed sequencing reads

Author(s)

Nicola Licheri and Giulio Ferrero

Examples

## Not run: 
...

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.