comprna/reorientexpress: first release
Description
This is the first release of ReorientExpress, a program to create, test and apply models to predict the 5'-to-3' orientation of long-reads from cDNA sequencing with Nanopore or PacBio using deep neural networks for samples without a genome or a transcriptome reference. 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).
Files
comprna/reorientexpress-v1.0.0.zip
Files
(78.3 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/comprna/reorientexpress/tree/v1.0.0 (URL)