Does Matlab support bed, wig, and other usual genomics file formats?

I'm curious if the new version of Matlab (2014b) added support for the usual genomics file formats: bed, wig, bedGraph, BigWig? Is there any function to import/export from/to these formats?

Answer 1

[Jon Boerner]

I took a quick look through the documentation, and was not able to find anything about those file types. The pages that describe the import/export capabilities are:

• Sequence Analysis Data Import and Export
• Mass Spectrometry and Bioanalytics Data Import and Export
• High Throughput Sequencing Data Import and Management
• Microarray Analysis Data Import and Management

Looking at those pages, the file formats that are supported appear to be:

• FASTA
• GenBank
• GenPept
• EMBL
• BLAST
• PDB
• PFAM
• ClustalW
• GCG
• PHYLIP
• Newick
• FASTQ
• MZCDF
• MZXML
• JCAMP
• TGSPC
• SFF
• SCF
• SAM
• BAM
• SOAP
• Bowtie
• Affymetrix® GeneChip®
• Illumina®
• Agilent®
• Gene Expression Omnibus (GEO)
• ImaGene®
• SPOT
• GenePix® GPR
• GAL

Notice the section with SAM, BAM, FASTA, FASTQ, SOAP, and Bowtie files (the most relevant for genomic work).

I do not see any mention of the formats you mentioned.

One good place to look for new features in any given release is the release notes (if you were not already aware). For the Bioinformatics toolbox, the release notes can be found here.

Again, there is not any mention there of the file formats you specified.

[Razvan]

That's too bad. In my field, after fastq and bam, the most used file formats are bed, wig, bedgraph and bigwig (all described here: http://genome.ucsc.edu/FAQ/FAQformat.html). Maybe with the next Matlab update...