DeepMod2
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WGLab
DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
**i am getting this error if i run from umbutu** Traceback (most recent call last): File "/mnt/c/DeepMod2/raw_data/deepmod2/train/generate_features.py", line 10, in from numba import jit ModuleNotFoundError: No module named 'numba' but...
Hi, Would DeepMod2 be able to pinpoint locations where uncharacterised modifications are present? The current base callers can not handle this, because not trained for these. But being able to...
 I have indexed and aligned my BAM file still it gives the above error. When I let the command run it produced an empty file.
Hello there, I re-post an issue I posted in DeepMod regarding future plan to include detection of other methylation motives in plant. Hope it can be one of the new...
Any insight in what is causing this error would be appreciated. Thanks, Arkadiy ``` Command: python /data/MAB/bin/DeepMod2/deepmod2 detect-guppy --threads 24 --fast5 ../../../fast5_pass/single_barcode12 --ref assembly.fasta --bam assembly.bam RuntimeError: module compiled against...
Hello, Thanks for your great efforts to develop a series of useful tools detecting methylation across the genome, including DeepMod and DeepMod2. The first question is: do you assess the...
When I go through the first step (the command as guppy_basecaller -i fast5_pass/ -c ~/biosoft/ont-guppy-cpu/data/dna_r10.4.1_e8.2_400bps_sup.cfg --num_callers 10 --cpu_threads_per_caller 5 --save_path fastq --bam_out --moves_out basecall.bam) to get the basecaller.bam file, I...
when running `deepmod2 detect --model 'transformer_r10.4.1_5khz_v4.3'`, it throws error like: > Traceback (most recent call last): File "/hpcf/authorized_apps/rhel8_apps/deepmod2/install/deepmod2-env2/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/hpcf/authorized_apps/rhel8_apps/deepmod2/install/deepmod2-env2/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args,...
I have a bam file which was basecalled by Dorado, and I try to run deepmod2 on it using the latest model bilstm_r10.4.1_5khz_v4.3. However the Dorado basecalling used for that...
I encountered an error. Could you please help? `ModuleNotFoundError: No module named 'tensorflow.keras'` Thanks, Taha
