Documentation

This is machine translation

Translated by Microsoft
Mouseover text to see original. Click the button below to return to the English verison of the page.

Note: This page has been translated by MathWorks. Please click here
To view all translated materals including this page, select Japan from the country navigator on the bottom of this page.

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

expand all

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)
ans = 

  Axes (Quality Stratification) with properties:

             XLim: [0.1000 41]
             YLim: [0 100]
           XScale: 'linear'
           YScale: 'linear'
    GridLineStyle: '-'
         Position: [0.1300 0.1100 0.7750 0.8150]
            Units: 'normalized'

  Use GET to show all properties

Was this topic helpful?