Function to execute Cutadapt on RNA-Seq reads

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

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

Nicola Licheri and Giulio Ferrero

Examples

if (FALSE) {
...
}