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Error following matlab's working with genomes

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I tried following matlab's exapmle of how to memmorry map a genome file ( https://www.mathworks.com/help/bioinfo/examples/working-with-whole-genome-data.html ), but am getting the foollowing error -
Array indices must be positive integers or logical values.
Error in nt2int (line 92)
seq = map((uint8(nt) + 1) - uint8('a'));
I am using 'hg38.fa' from the UCSC genome browser.
Thank you,
Guy
  6 Comments
Walter Roberson
Walter Roberson on 12 Sep 2020
Unfortunately that is timing out for me today.

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Accepted Answer

Guy Nir
Guy Nir on 13 Sep 2020
I added a command to remove any character which is not a letter:
% Remove numbers
numIdx=find(~isletter(charData));
charData(numIdx)='';
% Convert to integers
intData = nt2int(charData);
I think Matlab should consider adjusting some of their functions to whole-genome files (instead of whole chromosmes). Other algorithms use these numbers within the FASTA file for info about these sequences.

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