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awesome-nanopore's Issues

A new tool for RNA modification analysis

Hi,

A new tool, DENA (https://github.com/weir12/DENA) (Qin, H., Ou, L., Gao, J. et al. DENA: training an authentic neural network model using Nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6-methyladenosine on RNA. Genome Biol 23, 25 (2022). https://doi.org/10.1186/s13059-021-02598-3), that was developed by our group, can be used for RNA modification analysis. Perhaps you can add it to the corresponding list.

Best,

Hang

Translating Raw Data into a deep-learning trainable format

Hi,

Thank you so much for putting together this curated list of nanopore software. I'm investigating ways to convert raw nanopore data (.fast5 files) and associated sequences (.fasta files) into a format that can be fed into a deep learning algorithm. SACall, for example, requires input to be numpy-specific signal and label files - but fails to demonstrate how it made the conversion from this dataset to numpy arrays.

Do you know if those kinds of software packages exist and how that would be best accomplished?

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