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xiaochuanle / hifimeth

High-fidelity 5mC DNA methylation detection model for PacBio HiFi reads
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Whether gcn5MC can be used in plant genomes #1

Closed chenchen-eng closed 1 year ago

chenchen-eng commented 1 year ago

hello Mr Le,I'm doing research on plant genomes, and I want to ask if I can use them in plant genomes?Thanks

aragornwubo commented 1 year ago

It was trained on human CCS data and works on CpG motifs of different animals. I haven't tried it on plant data. In theory it should work on plant CpG motif, but not CHH or CHG motif right now.

xiaochuanle commented 1 year ago

We have added two examples on plant genomes to validate the applicability of hifimeth on plant genomes. See https://github.com/xiaochuanle/hifimeth/tree/master/examples-arab and https://github.com/xiaochuanle/hifimeth/tree/master/examples-oryza.

chenchen-eng commented 1 year ago

Thank you so much  

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------------------ 原始邮件 ------------------ 发件人: "Chuan-Le @.>; 发送时间: 2023年6月8日(星期四) 晚上9:50 收件人: @.>; 抄送: @.>; @.>; 主题: Re: [xiaochuanle/hifimeth] Whether gcn5MC can be used in plant genomes (Issue #1)

We have added two examples on plant genomes to validate the applicability of hifimeth on plant genomes. See https://github.com/xiaochuanle/hifimeth/tree/master/examples-arab and https://github.com/xiaochuanle/hifimeth/tree/master/examples-oryza.

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