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How do I download a Reference Genome

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smsinks
smsinks on 31 Jul 2017
Commented: Akhilesh Thakur on 31 Jul 2017
I am going walking through a MATLAB example for Exploring Genome Wide Methylation... The instructions go like this:
This example also assumes that you downloaded the reference human genome (GRCh37.p5). You can use the bowtie-inspect command to reconstruct the human reference directly from the bowtie indices. Or you may download the reference from the NCBI repository by uncommenting the following line:
% getgenbank('NC_000009','FileFormat','fasta','tofile','hsch9.fasta');
How ever this line of code produces an error as shown below:
Error using getncbidata (line 191) The key NC_000009 was not found in the nucleotide database at this time. Check that the input is a valid Accession Number.
Note: This function is dependent on NCBI's Entrez tools and sequence databases. Changes to either may cause this function to break.
Error in getgenbank (line 70) [varargout{1:nargout}] = getncbidata(accessnum,'fileformat','GenBank','database','nucleotide',varargin{:});
The accession number seem okay, as I have checked the NCBI website.
Does anyone know how to do this right?
Cheers.

  1 Comment

Akhilesh Thakur
Akhilesh Thakur on 31 Jul 2017
https://www.mathworks.com/help/bioinfo/examples/working-with-whole-genome-data.html https://www.mathworks.com/help/bioinfo/examples/comparing-whole-genomes.html#zmw57dd0e13135 Did you check this links?

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