ngsbrowser - Open NGS Browser to visualize and explore short-read sequence alignments

Syntax

Description

ngsbrowser opens an empty session of the NGS Browser, from which you can import:

• A single reference sequence from a FASTA-formatted file

• Short-read sequence alignment data from SAM- or BAM-formatted files or BioMap objects

• Annotation features from GFF- or GTF-formatted files

You can then use the NGS Browser to visualize and explore the alignments and feature annotations.

Tips

• Use the NGS Browser to compare the alignment of multiple data sets to a common reference sequence.

• Use the NGS Browser to investigate regions of interest in the short-read alignment determined by various analyses, such as RNA-Seq, ChIP-Seq, and genetic variation analyses.

Examples

Create a BioMap object from a SAM-formatted file, open the NGS Browser, and then import the short-read alignment data from the BioMap object:

b = BioMap('ex1.sam');
ngsbrowser

Import the BioMap object, b, into the browser by selecting File > Import Alignment Data from MATLAB Workspace.

See Also

BioMap | multialignviewer | seqtool

Tutorials

• Identifying Differentially Expressed Genes from RNA-Seq Data
• Exploring Protein-DNA Binding Sites from Paired-End ChIP-Seq Data

How To

• Visualizing and Investigating Short-Read Alignments

Related Links

• Bowtie
• Burrows-Wheeler Aligner
• SAMtools
• NCBI Genome Database

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