align_free_quan: Alignment-free expression quantification with Salmon at gene...

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

Alignment-free expression quantification with Salmon at gene and transcript levels.

Description

Alignment-free expression quantification with Salmon at gene and transcript levels.

Usage

align_free_quan(
  pair,
  genome,
  transcript,
  annotation,
  threads = 4,
  salmon_index_add = NULL,
  salmon_quan_add = NULL
)

Arguments

pair	'single' for single-end (SE) or 'paired' for paired-end (PE) reads.
genome	the reference genome.
transcript	the reference transcript
annotation	the annotation file.
threads	the number of threads to be used. Default is 4.
salmon_index_add	additional parameters to customize salmon index command. Default is NULL.
salmon_quan_add	additional parameters to customize salmon quan command. Default is NULL.

Value

None

Examples

align_free_quan(
pair = 'paired', 'test_Homo_sapiens.fna', 
'test_transcript_Homo_sapiens.fna','test_Homo_sapiens.gff'
)

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