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pod5 to fast5 and nanopolish call-methylation no reult #1116

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fhy1203 opened this issue Oct 11, 2023 · 4 comments
Open

pod5 to fast5 and nanopolish call-methylation no reult #1116

fhy1203 opened this issue Oct 11, 2023 · 4 comments

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@fhy1203
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fhy1203 commented Oct 11, 2023

Hi,
My data is pod5 data.And I converted the pod5 data to fast5 data and analyzed it using nanopolish,but there is no result in naopolish result。Here is my code and log information。
nanopolish call-methylation -t 4 -r J-365033-ZM-3.all.fastq -b J-365033-ZM-3.merge.Y.bam -g /mnt/data/human_g1k_v37.fasta > methylation_calls.tsv
### [post-run summary] total reads: 52290, unparseable: 0, qc fail: 0, could not calibrate: 0, no alignment: 52290, bad fast5: 171

@hasindu2008
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Is this r10.4.1 data?

@fhy1203
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fhy1203 commented Oct 11, 2023

Is this r10.4.1 data?

Yes,my data is r10.4.1 data

@hasindu2008
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Nanopolish doesn't support R10.4.1 at the moment at the moment I think. You could try f5c, which is the same method as nanopolish but also has an R10.4.1 model.

@fhy1203
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fhy1203 commented Oct 11, 2023

Nanopolish doesn't support R10.4.1 at the moment at the moment I think. You could try f5c, which is the same method as nanopolish but also has an R10.4.1 model.

Thank you and I will try

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