fastqread - Read data from FASTQ file

Syntax

FASTQStruct = fastqread(File) [Header, Sequence] = fastqread(File) [Header, Sequence, Qual] = fastqread(File) fastqread(..., 'Blockread', BlockreadValue, ...) fastqread(..., 'HeaderOnly', HeaderOnlyValue, ...)

Description

FASTQStruct = fastqread(File) reads a FASTQ-formatted file and returns the data in a MATLAB array of structures.

[Header, Sequence] = fastqread(File) returns only the header and sequence data in two separate variables.

[Header, Sequence, Qual] = fastqread(File) returns the data in three separate variables.

fastqread(..., 'PropertyName', PropertyValue, ...) calls fastqread with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Enclose each PropertyName in single quotation marks. Each PropertyName is case insensitive. These property name/property value pairs are as follows:

fastqread(..., 'Blockread', BlockreadValue, ...) reads a single sequence entry or block of sequence entries from a FASTQ-formatted file containing multiple sequences.

fastqread(..., 'HeaderOnly', HeaderOnlyValue, ...) specifies whether to return only the header information.

Inputs

`File`	String specifying a file name or path and file name of a FASTQ-formatted file. If you specify only a file name, that file must be on the MATLAB search path or in the current folder.
`BlockreadValue`	Scalar or vector that controls the reading of a single sequence entry or block of sequence entries from a FASTQ-formatted file containing multiple sequences. Enter a scalar `N`, to read the `N`th entry in the file. Enter a 1-by-2 vector [`M1, M2`], to read a block of entries starting at the `M1` entry and ending at the `M2` entry. To read all remaining entries in the file starting at the `M1` entry, enter a positive value for `M1` and enter `Inf` for `M2`.
`HeaderOnlyValue`	Specifies whether to return only the header information. Choices are `true` or `false` (default).

Outputs

FASTQStruct

Array of structures containing information from a FASTQ-formatted file. There is one structure for each read or entry in the file. Each structure contains the following fields.

Field Description

Header Header information.

Sequence Single letter-code representation of nucleotide sequence.

Quality ASCII representation of per-base quality scores for a nucleotide sequence.

Header

Variable containing header information or, if the FASTQ-formatted file contains multiple sequences, a cell array containing header information.

Sequence

Variable containing sequence information or, if the FASTQ-formatted file contains multiple sequences, a cell array containing sequence information.

Qual

Variable containing quality information or, if the FASTQ-formatted file contains multiple sequences, a cell array containing quality information.

Definitions

A FASTQ-formatted file contains nucleotide sequence and quality information on four lines:

Line 1 — Header information prefixed with an @ symbol
Line 2 — Nucleotide sequence
Line 3 — Header information prefixed with a + symbol
Line 4 — ASCII representation of per-base quality scores for the nucleotide sequence using Phred or Solexa encoding

Examples

Read a FASTQ file into an array of structures:

% Read the contents of a FASTQ-formatted file into
% an array of structures
reads = fastqread('SRR005164_1_50.fastq')

reads = 

1x50 struct array with fields:
    Header
    Sequence
    Quality

Read a FASTQ file into three separate variables:

% Read the contents of a FASTQ-formatted file into 
% three separate variables
[h,s,q] = fastqread('SRR005164_1_50.fastq');

Read a block of entries from a FASTQ file:

% Read the contents of reads 5 through 10 into
% an array of structures
reads_5_10 = fastqread('SRR005164_1_50.fastq', 'blockread', [5 10])

1x6 struct array with fields:
    Header
    Sequence
    Quality

Tutorials

Working with Illumina/Solexa Next-Generation Sequencing Data