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
`bamindexread`	Read BAM Index, BAI, file

Classes

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BioRead and BioMap

`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

GTF and GFF Annotations

`GFFAnnotation`	Contain General Feature Format (GFF) annotations
`GTFAnnotation`	Contain Gene Transfer Format (GTF) annotations
`cuffgffread`	Filter and convert GFF and GTF files
`cuffgtf2sam`	Convert GTF files to SAM files

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

Use the Genomics Viewer app to view NGS alignment data for single nucleotide variation in cytochrome p450 gene.