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It is in general uncertain whether software that has been written to process standard XYZ files lacking annotations could successfully cope with this additional content.
In practice, we found that data providers could easily produce text files containing data as comma separated values in the format which we specified, and which the distributed software has been written to process.
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A time convolution program was written to process the data produced and simulate more realistic pile-up.
Custom calculators were written to process the HCS data and perform the z-score and B-score statistical analysis [67], [68].
Filter rules can then be written to process this new type of event.
A Perl script was written to process the mapping results and generate the gene expression profile.
Programs were written to process this training data into feature vector form.
A Perl script was written to process the pair-wise alignments and enumerate the sequence polymorphisms (SNPs, insertions, deletions, etc).
A Java Programme BuildRefHapInput.V1.1.jar was written to process gff3 files of scaffold co-ordinates and Variant Call Format (VCF) files of SNP and output the frag and allvars files for processing by the SIH programme [ 14].
Programs were written to process training sequences into feature vector form for the training of three SVM classifiers: SVM T 1, SVM T 2, and SVM FL (Additional File 3).
For whole process a code has been written to make the process of filtering, sorting, sifting, combining and tagging automated.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com