bowtie_align: RACEseq BOWTIE alignment function

In pantastheo/RACEseqR: Downstream analysis R package for 5-RACE Next Generation Sequencing experiments

Description

Function to perform the trimming of the RACE adapter using CUTADAPT and the alignment of the sequencing data from the .fastq files using the BOWTIE aligner.

Usage

bowtie_align(input_data, replicon_ref, mismatch, RACE_adapter, out_name)

Arguments

input_data	The input .fastq files to be used for the alignment.
replicon_ref	The reference sequence to be used in the alignment.
mismatch	The number of mismatches to be allowed during alignment.
RACE_adapter	The RACE adapter nucleotide sequence to be trimmed from the reads using cutadapt.
out_name	The output filename from the alignment.

See Also

tmap_align

Examples

bowtie_align()

pantastheo/RACEseqR documentation built on May 12, 2019, 6:16 p.m.