goodBaseQuality: Filters out sequences which have bad base quality readings.

In valenlab/amplican: Automated analysis of CRISPR experiments

Filters out sequences which have bad base quality readings.

Description

Filters out sequences which have bad base quality readings.

Usage

goodBaseQuality(reads, min = 20, batch_size = 1e+07)

Arguments

reads	(ShortRead object) Loaded reads from fastq.
min	(numeric) This is the minimum quality that we accept for every nucleotide. For example, if we have a sequence with nucleotides which have quality 50-50-50-50-10, and we set the minimum to 30, the whole sequence will be a bad sequence.
batch_size	(numeric) How many reads to process at a time.

Value

(boolean) Logical vector with the valid rows as TRUE.

valenlab/amplican documentation built on Jan. 28, 2024, 5:10 a.m.