quality_trim: Trim poor quality samples using cutadapt.

In sunshanwen/BP4RNAseq: A babysitter's package for reproducible RNA-seq analysis

Trim poor quality samples using cutadapt.

Description

Trim poor quality samples using cutadapt based on the results from quality_test().

Usage

quality_trim(
  per_base,
  per_seq,
  pair,
  threads = 4,
  scRNA = FALSE,
  cutadapt_add = NULL
)

Arguments

per_base	samples with poor per base sequence quality.
per_seq	samples with poor per sequence quality scores.
pair	'single' for single-end (SE) or 'paired' for paired-end (PE) reads.
threads	the number of threads to be used. Default is 4.
scRNA	logic, whether single-cell RNA-seq is quantified or not. Default is FALSE.
cutadapt_add	additional parameters to customize cutadapt to trim poor quality reads. Default is NULL

Value

None

Examples

quality_trim(per_base = 'test_read_2.fastq', per_seq = 'test_read_2.fastq',
             pair = 'paired', threads = 4, scRNA = TRUE)

sunshanwen/BP4RNAseq documentation built on March 28, 2022, 5:35 p.m.