8000 Can pipeline be run from FASTQ files rather than FAST5 for CpG analysis? · Issue #159 · LabShengLi/nanome · GitHub
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Can pipeline be run from FASTQ files rather than FAST5 for CpG analysis? #159

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alexlancaster opened this issue Feb 19, 2025 · 1 comment
Open

Can pipeline be run from FASTQ files rather than FAST5 for CpG analysis? #159

alexlancaster opened this issue Feb 19, 2025 · 1 comment

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@alexlancaster
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If you already have FASTQ files - can the pipeline be run from the FASTQ files onwards - rather than the raw FAST5 files? I am interested in CpG island and I don't want to have to go back to the raw FAST5 files.
@liuyang2006
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Hi @alexlancaster,

The FASTQ file itself does not include Nanopore current signal data, which is necessary for predicting 5mC/5C. The current pipeline has not yet support methylation calling at CpG islands only.

Best,
Yang

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@alexlancaster @liuyang2006
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