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hasindu2008 / f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
https://hasindu2008.github.io/f5c/docs/overview
MIT License
144 stars 26 forks source link

5fc index --sequencing_summary #93

Closed will-NYGC closed 3 years ago

will-NYGC commented 3 years ago

Can you clarify the issues with the sequencing_summary option? It speeds things up enormously and so I hope to keep using it if possible. What exactly are the formatting issues and/or the proper format specifications for sequencing_summary.txt.

hasindu2008 commented 3 years ago

Hi

sequencing_summary.txt is a file generated by ONT's MinKNOW and unfortunately, it does not have any specification (even it should have one!) and keeps changing frequently. So this option needs to be updated whenever ONT changes the sequencing summary format. Are you encountering any problems with it?

will-NYGC commented 3 years ago

We haven't had problems yet but just noticed the warning in the documentation. Will it error out if there's an issue? Or will the output be wrong? As long as it's causing easily detectable problems, I think it's worth it to us to keep using it.

hasindu2008 commented 3 years ago

Yes, it will error out if there is an issue and will not affect the output. The sequencing summary file's use is to quickly determine which read ID maps to which fast5 file. If the corresponding column name in the sequencing summary changed, f5c will not be able to use the summary file and will anyway fall back to the default method.

will-NYGC commented 3 years ago

ok thanks, i think you can close this issue then. On Oct 1, 2021, 8:48 PM -0400, Hasindu Gamaarachchi @.***>, wrote:

Yes, it will error out if there is an issue and will not affect the output. The sequencing summary file's use is to quickly determine which read ID maps to which fast5 file. If the corresponding column name in the sequencing summary changed, f5c will not be able to use the summary file and will anyway fall back to the default method. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

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hasindu2008 commented 3 years ago

No problem. Feel free to reopen or open a new issue if you have any more questions in the future.