Nan error in RNA-ATAC integration
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- Dominant language
- Python
- Stars
- 323
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Description
Dear kaizhang,
Hello, I am a graduate student in UST-KRIBB school in South Korea. First, thank you for your effort in bioinformatics study.
I am trying to integrate scRNA-seq data and scATAC-seq data with snapatac2. I concatenate two, and made vae model. However, I cannot train this model. There are Nan error still occurs, so I am not able to move on next step.
Here are my datasets:
If you need more information, please let me know.
Have a nice day.
From, HOKYOUNG KWAK
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Research direction
The report provides dataset images but no code, versions, traceback, or named files. Start by reproducing the scRNA-seq and scATAC-seq concatenation followed by VAE training, then identify where NaN values first appear. Done means the failure is reproducible with sufficient details and either training succeeds or the cause is documented.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100