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sarahet / RLM

Read level DNA methylation analysis of bisulfite converted sequencing data
BSD 3-Clause "New" or "Revised" License
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CHH and CHG Methylation Rate #8

Closed sal123butrus closed 1 hour ago

sal123butrus commented 2 weeks ago

Hello! Thank you for developing this great tool. I was wondering if there is an option to output information about CHH and CHG methylation. This would be used to assess the efficiency of bisulfite conversion in each sample.

Thanks, Salwan

sarahet commented 1 day ago

Hi Salwan,

Sorry for the late reply! This is unfortunately not planned as we would expect users to generally also run a standard methylation caller for their analysis (given that RLM only outputs drastically filtered results where only reads covering at least 3 CpG are considered). These tools should then also give you an estimate of CHH and CHG methylation. Given the filtering within RLM, the CHH/CHG rate would also probably be falsified and could not provide you with a solid estimate of the bisulfites conversion efficiency.

Best, Sara

sal123butrus commented 1 hour ago

Makes sense, thanks!