adapter_trim: Trim samples with adapter using cutadapt.

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

Trim samples with adapter using cutadapt.

Description

Trim samples with adapter using cutadapt based on the results from quality_test().

Usage

adapter_trim(sample, pair, threads = 4, scRNA = FALSE, cutadapt_add = NULL)

Arguments

sample	samples with adapter.
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 adapter. Default is NULL.

Value

None

Examples

adapter_trim(sample = 'test_read_2.fastq', pair = 'paired', scRNA = TRUE)

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