fastqread

Read data from FASTQ file

Syntax

FASTQStruct = fastqread(File)

[Header,Sequence] = fastqread(File)

[Header,Sequence,Qual] = fastqread(File)

___ = fastqread(File,Name=Value)

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(File,Name=Value) specifies options using one or more name-value arguments in addition to the input arguments in previous syntaxes. For example, to return only the header information, set HeaderOnlyValue to true.

Examples

Read FASTQ File into Array of Structures

FASTQStruct = fastqread("SRR005164_1_50.fastq")

FASTQStruct=1×50 struct array with fields:
    Header
    Sequence
    Quality

Read FASTQ File into Three Separate Variables

[Header,Sequence,Qual] = fastqread("SRR005164_1_50.fastq");
whos Header Sequence Qual

  Name          Size            Bytes  Class    Attributes

  Header        1x50             9734  cell               
  Qual          1x50            18668  cell               
  Sequence      1x50            18668  cell               

Read Block of Entries from FASTQ File

FASTQStruct_5_10 = fastqread("SRR005164_1_50.fastq",BlockRead=[5 10])

FASTQStruct_5_10=1×6 struct array with fields:
    Header
    Sequence
    Quality

Input Arguments

File — Name of FASTQ-formatted file

string scalar | character vector

Name of FASTQ-formatted file, specified as a string scalar or character vector. If you specify only a file name, then that file must be on the MATLAB search path or in the MATLAB current folder. Otherwise, specify the full or relative path name.

Example: "myFile.fastq"

Example: "myDir\myFile.fastq"

Example: "C:\myDir\mySubdir\myFile.fastq"

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is 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.

Example: fastqread("SRR005164_1_50.fastq",HeaderOnly=true)

Blockread — Sequence entries to read

positive integer scalar | two-element vector of positive integers or Inf values

Sequence entries to read, specified as a positive integer scalar or a two-element vector of positive integers or Inf values. Specify Blockread in one of these three ways:

• Positive integer scalar N — Read Nth entry from the file.

• Two-element vector of positive integers [N1,N2] — Read a block of entries starting at the N1st entry and ending at the N2nd entry from the file.

• Two-element vector of the form [N,Inf] — Read all entries starting at the Nth entry from the file.

Example: 1

Example: [2 4]

Example: [5 Inf]

Data Types: double | single | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64

HeaderOnly — Whether to return only the header information

false or 0 (default) | true or 1

Whether to return only the header information, specified as a numeric or logical 0 (false) or 1 (true).

Data Types: logical | double | single | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64

TrimHeadersValue — Whether to trim the header

false or 0 (default) | true or 1

Whether to return only the header information, specified as a numeric or logical 0 (false) or 1 (true). If you specify TrimHeadersValue as true, the headers will be trimmed after their first white space characters. White space characters include the space (char(32)) and tab (char(9)) characters.

Data Types: logical | double | single | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64

Output Arguments

FASTQStruct — Sequence data

structure array

Sequence data, returned as a structure array. There is one array entry for each sequence read or entry in the file. Each entry of the structure array contains Header, Sequence, and Qual fields.

Header — Header information

character vector | cell array of character vectors

Header information, returned as a character vector or cell array of character vectors.

Sequence — Sequence information

character vector | cell array of character vectors

Sequence information, returned as a character vector or cell array of character vectors.

Qual — Quality information

character vector | cell array of character vectors

Quality information, returned as a character vector or cell array of character vectors.

More About

FASTQ-file Format

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

Version History

Introduced in R2009b