Comments (2)
kishwarshafin
commented on June 18, 2024
Hi @yipukangda ,
This sounds very interesting, and thanks for choosing MP/HELEN for your experiment. If this is a new channel and the error mode is different, I'd suggest you try PEPPER (https://github.com/kishwarshafin/pepper) to train and test your new pore. The reason would be simplicity and a faster trial-error loop. If you open an issue there or send me an email at [email protected], I can help you with setting up a training run.
Things you need to train a polisher:
- A truth assembly (high-quality assembly that can be regarded as the truth)
- A draft assembly (an assembly that you are trying to improve)
- Reads aligned to the draft assembly.
If you have these, open an issue in PEPPER repository and I will help you with that.
from helen.
yipukangda
commented on June 18, 2024
@kishwarshafin Thanks a lot, I will read the manual and open an issue soon.
from helen.
Related Issues (20)
- Plant species HOT 3
- MarginPolish HOT 3
- margin docker run fail HOT 27
- Issue on stitch.py HOT 7
- Compatibility with draft assembly from other assemblers HOT 3
- Models for Guppy 3.6 HOT 2
- some problem occurs when evaluating the data of na12878 chromosome 21 HOT 4
- Add helen to bioconda. HOT 5
- Are existing models suitable to polish a high heterozygosity plant genome assemblies? HOT 3
- marginpolish docker stuck at 99% HOT 13
- How to install helen in a gcc4.8 enrivments? HOT 3
- MarginPolish output zero .fa file HOT 9
- torch.set_num_threads error in docker image HOT 3
- Exception: process 6 terminated with signal SIGKILL HOT 5
- wrong script in example Usage in README.md HOT 1
- Only Polish interested sequences HOT 3
- Question about model's training data HOT 2
- there are no other mammal models other than human? HOT 2
- helen polish UserWarning on batch size
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from helen.