truncate_sequences.quality_score {LocaTT}

Truncate DNA Sequences at Specified Quality Score

Description

Truncates DNA sequences immediately prior to the first occurrence of a Phred quality score being equal to or less than a specified value.

Usage

truncate_sequences.quality_score(sequences, quality_scores, threshold = 3)

Arguments

sequences

A character vector of DNA sequences to truncate.

quality_scores

A character vector of DNA sequence quality scores encoded in Sanger format.

threshold

Numeric. The Phred quality score threshold used for truncation. The default is 3 (i.e., each base in a trimmed sequence has a greater than 50% probability of having been called correctly).

Value

A list containing two elements. The first element is a character vector of truncated DNA sequences, and the second element is a character vector of quality scores which have been truncated to their corresponding truncated DNA sequences.

See Also

truncate_sequences.length for truncating DNA sequences to a specified length.
truncate_sequences.probability for truncating DNA sequences by cumulative probability that all bases were called correctly.

Examples

truncate_sequences.quality_score(sequences=c("ATATAGCGCG","TGCCGATATA","ATCTATCACCGC"),
                                 quality_scores=c("989!.C;F@\"","A((#-#;,2F","HD8I/+67=1>?"),
                                 threshold=3)