DeepMod2

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Error！Deepmod2 analysis of human methylation

2

Hi, I encountered an error when I used the test BAM for analysis. It can't be resolved. I'm worried. Please help me. And our server does not have a GPU,The...

zzangcy

Encountering errors running aligned BAM files

6

I am trying to call 5mc on a bacterial genome and I am encountering the error below. I have run this genome on a Gridion R.10 flowcell and performed the...

tewing4

Empty output.per_site.aggregated and output.per_site files

1

Hello, I am using DeepMod 2 to detect methylation from pod5s produced using nanopore sequencing. However, the output.per_site.aggregated and output.per_site files are empty. I am following the tutorial described here...

MH-Raza

CMD: ```bash # cd to snakemake dir cd /data/nanopore THREADS="8" EQA_ID="202401" SAMPLE_ID="NP1_HF_1" conda activate deepmod2 time python resources/DeepMod2/deepmod2 detect \ --bam nanopore/bam_with_moves/${SAMPLE_ID}.bam \ --input uploaded/20250719/${EQA_ID}_pod5_pass \ --model transformer_r10.4.1_5khz_v5.0 \ --file_type...

YuanfengZhang

Hi， I'm trying to detect 5mC with deepmod2, with input files in fast5 format and basecalling with guppy. The basecalling cmd is: `guppy_basecaller -i /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/single_fast5_pass/dir_00/ -s /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/hg002.guppy/ -c ~/nanopore_methods/ont-guppy/data/dna_r10.4.1_e8.2_400bps_5khz_hac.cfg --bam_out...

Moretta1