count_primers: Count primers

In ucvm/nemabiomeR: Helper functions to run the dada2 pipeline on nemabiome data

Description

This function counts the number of times it finds a match to the given primer in a fastq file

Usage

count_primers(r1_files, fwd_primer, rev_primer, r2_files = NULL)

Arguments

r1_files	list of fastq files with the forward read
fwd_primer	forward primer sequence as a string
rev_primer	reverse primer sequence as a string
r2_files	list of fastq files with the reverse read, optional

Value

a tibble with the counts of the primers hits in different orientations, one row per file

ucvm/nemabiomeR documentation built on June 7, 2019, 12:50 a.m.