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plotPerPositionCountByQuality

Class: BioReadQualityStatistics

Plot fractions of reads with Phred scores in ranges

Syntax

plotPerPositionCountByQuality(QSObj)
H = plotPerPositionCountByQuality(QSObj)

Description

plotPerPositionCountByQuality(QSObj) generates a line plot displaying the fractions of all reads that have Phred scores in the ranges of 0–10, 11–20, 21–30, and 31–40 at each base position for the BioReadQualityStatistics object QSObj.

H = plotPerPositionCountByQuality(QSObj) returns the handle H to the axes object containing the generated plot.

Input Arguments

QSObj

BioReadQualityStatistics object.

Output Arguments

H

Handle to axes object containing generated plot.

Examples

Plot Fractions of Reads with Phred Scores in Ranges

Create a BioReadQualityStatistics object from a FASTQ file using only the first 40 characters of each read with a minimum average quality score of 5.

QSObj = BioReadQualityStatistics('SRR005164_1_50.fastq','FilterLength',40,'QualityScoreThreshold',5);

Plot the fractions of all reads with Phred scores in the ranges of 0–10, 11–20, 21–30, and 31–40 at each base position.

plotPerPositionCountByQuality(QSObj)

See Also

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