ReorientExpress: Reference-free orientation of nanopore cDNA reads with deep learning

Angel Ruiz-Reche,Akanksha Srivastava,Joel A. Indi,Ivan de la Rubia,Eduardo Eyras

Genome Biology（2019）

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摘要

We describe ReorientExpress (), a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep-learning to correctly predict the orientation of the majority of reads, and in particular when trained on a closely related species or in combination with read clustering. ReorientExpress enables long-read transcriptomics in non-model organisms and samples without a genome reference and without using additional technologies. * ONT : Oxford Nanopore Technologies DRS : Direct RNA sequencing cDNA : complementary DNA k-mer : length k oligomer DNN : Deep Neural Network MLP : Multi-layer perceptron CNN : Convolutional Neural Network IVT : In vitro transcribed PWM : Position Weight Matrix

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关键词

nanopore cdna,reads,deep learning,reference-free

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