Error following matlab's working with genomes

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Guy Nir 2020-9-12

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回答： Guy Nir 2020-9-13

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

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Walter Roberson 2020-9-12

Unfortunately that is timing out for me today.

Guy Nir 2020-9-12

Thank you for trying

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采纳的回答

Guy Nir 2020-9-13

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https://ww2.mathworks.cn/matlabcentral/answers/592681-error-following-matlab-s-working-with-genomes#answer_494029

在 MATLAB Online 中打开

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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