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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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How to get the label of Chlamydomonas reinhardtii. #48

Open Bessyyi opened 2 years ago

Bessyyi commented 2 years ago

Hello!@liuqianhn We borrowed Chlamydomonas reinhardtii to carry out experiments . However, I can't get the label of C. reinhardtii .We don't know whether all A is 6mA in motif GATC.What's more ,how did you divide the negative data set and the positive data set.Can you give me some suggestions.Thank you!

liuqianhn commented 2 years ago

@Bessyyi Sorry for the late reply. A could occur in different motif. Since deep learning is supervised learning, and thus, only the A in a motif for training will be used for testing. For C. reinhardtii, positive data is those A in a motif which have clear evidence determined by other methods, such as CHIP, and other A in the motif is considered as negative. Hope this answers your question.