Data Import

Import Next-Generation Sequencing (NGS) data and feature annotations from SAM, BAM, FASTA, FASTQ, GTF, and GFF files

Import NGS data stored in different file formats such as FASTA, FASTQ, SAM, and BAM files. Read feature annotations from GTF and GFF files. Use various objects to access and manage NGS data. For instance, the BioIndexedFile object lets you efficiently access text files with nonuniform-size entries, such as sequences and annotations. Use the object to access individual entries or a subset of entries when the source file is too big to fit in memory. Use the BioMap and BioRead objects to store and manage sequence read data containing information on headers, qualities, and alignments.

Functions

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FASTA

`fastainfo`	Return information about FASTA file
`fastaread`	Read data from FASTA file
`fastawrite`	Write to file using FASTA format

FASTQ

`fastqinfo`	Return information about FASTQ file
`fastqread`	Read data from FASTQ file
`fastqwrite`	Write to file using FASTQ format

SAM

`saminfo`	Return information about SAM file
`samsort`	Sort SAM files
`samread`	Read data from SAM file

BAM

`baminfo`	Return information about BAM file
`bamread`	Read data from BAM file
`bamsort`	Sort BAM files

GTF and GFF Annotations

`getData`	Create structure containing subset of data from `GTFAnnotation` or `GFFAnnotation` object
`getExons`	Return table of exons from `GTFAnnotation` object
`getFeatureNames`	Retrieve unique feature names from `GTFAnnotation` or `GFFAnnotation` object
`getGeneNames`	Retrieve unique gene names from `GTFAnnotation` object
`getGenes`	Return table of unique genes in `GTFAnnotation` object
`getIndex`	Return index array of annotations from `GTFAnnotation` or `GFFAnnotation` object
`getRange`	Retrieve range of annotations from `GTFAnnotation` or `GFFAnnotation` object
`getReferenceNames`	Retrieve reference names from `GTFAnnotation` or `GFFAnnotation` object
`getSegments`	Return table of non-overlapping segments from `GTFAnnotation` object
`getSubset`	Retrieve subset of elements from `GTFAnnotation` or `GFFAnnotation` object
`getTranscriptNames`	Retrieve unique transcript names from `GTFAnnotation` object
`getTranscripts`	Return table of unique transcripts in `GTFAnnotation` object
`cuffgffread`	Filter and convert GFF and GTF files
`cuffgtf2sam`	Convert GTF files to SAM files

SRA Toolkit

`srafasterqdump`	Download FASTQ or FASTA files from SRA (Since R2024a)
`SRAFasterqDumpOptions`	Option set for `srafasterqdump` (Since R2024a)
`srasamdump`	Download SAM files from SRA (Since R2024a)
`SRASAMDumpOptions`	Option set for `srasamdump` (Since R2024a)

Objects

`BioRead`	Contain sequence reads and their quality data
`BioMap`	Contain sequence, quality, alignment, and mapping data
`BioIndexedFile`	Allow quick and efficient access to large text file with nonuniform-size entries
`GFFAnnotation`	Contain General Feature Format (GFF) annotations
`GTFAnnotation`	Contain Gene Transfer Format (GTF) annotations

Topics

Work with Next-Generation Sequencing Data
Use BioIndexedFile objects to extract entries from large files using indices or keys, and parse data using custom functions.
Manage Sequence Read Data in Objects
Use BioMap and BioRead objects to access and manage Next-Generation Sequencing (NGS) data from various file formats, such as FASTQ, SAM, and BAM files.
Store and Manage Feature Annotations in Objects
Use GTF and GFF feature annotation objects to retrieve feature information from one or more reference sequences.
Data Formats and Databases
Access online databases and repositories using various MATLAB^® functions and import data to the workspace for further analyses.
Visualize NGS Data Using Genomics Viewer App
View NGS alignment data for single nucleotide variation in cytochrome p450 gene.

Featured Examples

Working with Illumina/Solexa Next-Generation Sequencing Data

Read and perform basic operations with data produced by the Illumina®/Solexa Genome Analyzer®.

Open Script