goodAvgQuality: This filters out sequences which have bad average quality...

In valenlab/amplican: Automated analysis of CRISPR experiments

This filters out sequences which have bad average quality readings.

Description

This filters out sequences which have bad average quality readings.

Usage

goodAvgQuality(reads, avg = 30, batch_size = 1e+07)

Arguments

reads	(ShortRead object) Loaded reads from fastq.
avg	(numeric) This is what the average score of the quality of sequence should be. For example, if we have a sequence with nucleotides which have quality 70-70-70, the average would be 70. If set the average to 70 or less the sequence will pass. If we set the average to 71 the sequence will not pass.
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.