Create quality control plots for sequence and quality data
seqqcplot( generates a figure with
quality control (QC) plots of sequence and quality data from
dataSource. The figure contains the following types of QC
Box plot for the average quality score at each sequence position
Bar plot for the sequence base composition at each sequence position
Histogram of the average sequence quality score distribution
Histogram of the GC-content distribution
Histogram of the sequence length distribution
In the figure, you can click a specific plot to open it in a separate window.
any of the input arguments in the previous syntaxes and additional
options specified by one or more
Create Quality Control Plots for Sequence and Quality Data
Plot quality control plots for sequence statistics and quality data from a FASTQ file.
Plot only the box plot of average quality score for each sequence position.
Plot the quality data of sequences with a minimum mean quality of 25.
Plot the data of sequences having a minimum mean quality of 25 and a minimum sequence length of 100.
Produce QC plots for the quality data corresponding to the subsequences from base position 10 to 100.
dataSource — Sequence and quality information
BioMap object |
BioRead object | character vector | string | string vector | cell array of character vector
Sequence and quality information, specified as a
BioRead object, character
vector, string, string vector, or cell array of character vectors
representing the names of FASTQ, SAM, or BAM files.
seqqcplot uses the read quality data, instead of the
alignment quality, if you specify SAM or BAM files, a
type — Name of QC plot to generate
'Summary' (default) |
Name of the QC plot to generate, specified as one of the following:
|Name of QC Plot||Description|
|Box plot for the average quality score at each sequence position.|
|Line plot for the sequence base composition at each sequence position.|
|Bar plot for the sequence base composition at each sequence position.|
|Histogram of the average sequence quality score distribution.|
|Histogram of the GC-content distribution.|
|Histogram of the sequence length distribution.|
|Summary figure containing all available QC plots, except the |
By default, all available QC plots are plotted as subplots in a figure. To open a specific subplot in a separate figure window, click the subplot.
encoding — Encoding format of base quality
'Illumina18' (default) |
Encoding format of the base quality, specified as one of the following:
Specify optional pairs of arguments as
the argument name and
Value is the corresponding value.
Name-value arguments must appear after other arguments, but the order of the
pairs does not matter.
Before R2021a, use commas to separate each name and value, and enclose
Name in quotes.
MeanQuality — Minimum threshold on average base quality across each sequence
-Inf (default) | numeric scalar
Minimum threshold on the average base quality across each sequence,
specified as a numeric scalar. The function considers only sequences
with average quality score equal to or greater than the threshold.
The threshold value is interpreted according to the specified encoding
format. Default is
-Inf, that is, any sequence
MinLength — Minimum threshold on sequence length
0 (default) | nonnegative numeric scalar
Minimum threshold on the sequence length, specified as a nonnegative numeric scalar. The function considers only sequences with length equal to or greater than the threshold.
BasePositions — Base position range for subsequences
[1 Inf] (default) | two-element vector
Base position range for subsequences, specified as a two-element
vector. The function considers only the subsequences in the specified
position range. Default is
[1 Inf], that is, the
entire length of each sequence is considered.
H — Handle to output figure
Handle to the output figure, returned as a figure handle.
Introduced in R2017a