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comprna/reorientexpress: first release

angelrure; Akanksha2511; Eduardo Eyras


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    <subfield code="a">&lt;p&gt;This is the first release of ReorientExpress,&amp;nbsp;a program to create, test and apply models to predict the 5&amp;#39;-to-3&amp;#39; orientation of long-reads from cDNA sequencing with Nanopore or PacBio using deep neural networks for samples without a genome or a transcriptome reference.&amp;nbsp;ReorientExpress implements two Deep Neural Network models: a Multi-Layer Perceptron (MLP) and a Convolutional Neural Network (CNN), and it uses as training input a transcriptome annotation from any species or any other fasta/fasq file of RNA/cDNA sequences for which the orientation is known. Training or testing data can thus be experimental data, annotation data or also mapped reads (providing the corresponding PAF file).&lt;/p&gt;</subfield>
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