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WGLab / DeepMod2

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
MIT License
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The basecalling and alignment can be performed separately? #7

Closed qiuyixmm closed 1 year ago

qiuyixmm commented 1 year ago

Hello, According to the Example, the basecallings and alignments were completed together. For the part of Methylation Calling from Guppy basecalled FAST5 files, the Guppy basecalled FAST5 files and BAM files containing alignments are required. Can I produce these two files separately as following steps: First, basecalled fast5 files and FQ files containing read sequences are generated using Guppy. Second, BAM files are generated by aligning FQ files to reference genome using minimap2. Third, the basecalled fast5 files and BAM files were fed to DeepMod2.

    Thanks!
umahsn commented 1 year ago

Hi,

Yes you can definitely separate basecalling and alignment steps. The example only does it in a combined way for the sake of brevity, but even in that case Guppy uses mnimap2 for alignment.

Best, Umair

qiuyixmm commented 1 year ago

Okay. Appreciated it! No questions here. I will close this issue.