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

bedbedgraphbigwigbioinformaticsBioinformatics Toolboxwig

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?

Best Answer

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:

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.

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MATLAB: Does the Bioinformatics Toolbox support Selenocysteine

This error occurs since the Bioinformatics Toolbox does not support the amino acid Selenocysteine with symbol 'U'. Hence NWALIGN fails.

The problem with alignment is that none of the standard scoring matrices for alignment include Selenocysteine. One possible workaround is to convert U to X (the symbol for 'any' amino acid) and then the alignment will not error out.

A code similar to the following can be used to avoid the error:

Seq1 =  'uarndcqeghilkumfpstwyv';
Seq2 =  'auurndcqeghilkmufpstwyv';
Seq1_X = strrep(Seq1,'u','x');
Seq2_X = strrep(Seq2,'u','x');
[score,alignment] = nwalign(Seq1_X,Seq2_X);
alignment = reshape(strrep(alignment(:)','X','U'),size(alignment));

MATLAB: Exploring Genome-wide Differences in DNA Methylation Profiles documentation

Hello,

Here you can find the pre-processing steps for starting the analysis outlined in the demo. Please note you must have bowtie installed and samtools available to you.

1. In the directories where you have saved your .sra files, do the following for each file:

fastq_dump SRRxxxx.sra

2. Download and uncompress the relevant bowtie indexes (pre-built indexes are available in the Bowtie website, just check the right-hand panel).

3. In each directory where you have your SRR* files, run bowtie against the reference genome. The options below specify you want only the best match (-m 1 --best), the result in SAM format (--sam), no more than 2 mismatches (-v), multithreading option (-p 8) and the time for each step (-t):

bowtie -t -q --sam -m 1 --best -k 1 -v 2 -p 8 /location_of_reference_index/hg18 SRRxxxx.fastq SRRxxxx.sam

4. Recover the reference as a fasta file (it's needed by the samtools' ordering)

bowtie-inspect hg18 > hg18.fasta

5. Convert to BAM and order

samtools view -bt hg18.fasta SRRxxxx.sam > SRRxxxxunordered.bam
samtools sort SRRxxxxunordered.bam SRRxxxx

Please let me know if you have further questions.

Best Answer

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MATLAB: Does the Bioinformatics Toolbox support Selenocysteine

MATLAB: Exploring Genome-wide Differences in DNA Methylation Profiles documentation

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