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WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
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Can DeepMod support multi-fast5 files? #18

Closed gongyh closed 4 years ago

gongyh commented 4 years ago

DeepMod gives out "Error!!! Channel information could not be found in UniqueGlobalKey/channel_id in ..." error when i use multi-fast5 files as input, but when i split them using "multi_to_single_fast5", it cannot detect events file the generated single fast5 files. Should i redo basecalling after spliting multi-fast5? Or there are other potential issues?

liuqianhn commented 4 years ago

Hi @gongyh , DeepMod does not support multi-fast5 now. One possible solution is to use ONT API to convert multi-fast5 to single fast5, and then re-basecall them. I have been working on the improvement version to support multi-fast5, but I cannot make it publicly available soon. Feel free to let me know if you have more questions.

gongyh commented 4 years ago

Thanks for your quick reply. I will re-basecall those splitted fast5 using albacore and try again.