plotPerSequenceGC

Class: BioReadQualityStatistics

Plot G or C nucleotide distribution

Syntax

plotPerSequenceGC(QSObj)
H = plotPerSequenceGC(QSObj)

Description

plotPerSequenceGC(QSObj) displays a bar graph showing the distribution of G or C content for short-read sequences of the BioReadQualityStatistics object QSObj.

H = plotPerSequenceGC(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

Plot G or C Nucleotide Distribution

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 G or C distribution.

plotPerSequenceGC(QSObj)
ans = 

  Axes (GC Distribution) with properties:

             XLim: [0 100]
             YLim: [0 18]
           XScale: 'linear'
           YScale: 'linear'
    GridLineStyle: '-'
         Position: [0.1300 0.1100 0.7750 0.8150]
            Units: 'normalized'

  Use GET to show all properties

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