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Psy-Fer / SquiggleKit

SquiggleKit: A toolkit for manipulating nanopore signal data
MIT License
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Running into issues with SquigglePlot.py using fast5 files converted from pod5 #65

Closed yinyuanmtu closed 5 months ago

yinyuanmtu commented 5 months ago

Is there a way to make it work with the these converted fast5 files? Thanks!

Psy-Fer commented 5 months ago

Hello,

Try using blue-crab to convert pod5 to slow5 instead.

Fast5 was modified too many times by ONT to be stable for ongoing support.

Cheers, James

yinyuanmtu commented 5 months ago

Hi James, Thanks! Does SquigglePlot.py take slow5 files or slow5 files need to be converted to fast5 files in order to run SquigglePlot? Thanks, Yinan

Yinan Yuan, PhD Assistant Professor in Forest Tree Genetics, Genomics and Biotechnology College of Forest Resources and Environmental Science Michigan Technological University Phone: 906-487-1835

On Tue, Apr 30, 2024 at 11:40 PM James Ferguson @.***> wrote:

Hello,

Try using blue-crab to convert pod5 to slow5 instead.

Fast5 was modified too many times by ONT to be stable for ongoing support.

Cheers, James

— Reply to this email directly, view it on GitHub https://github.com/Psy-Fer/SquiggleKit/issues/65#issuecomment-2087930483, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUXV276PWEPRACG62FPYN7DZABP4VAVCNFSM6AAAAABHBMUJT6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBXHEZTANBYGM . You are receiving this because you authored the thread.Message ID: @.***>

Psy-Fer commented 5 months ago

Hello,

squigglePlot can take slow5/blow5 files directly

In the help of the script under "-w", "--slow5",

James

yinyuanmtu commented 5 months ago

Great to know! Thanks alot James! Yinan Yuan, PhD Assistant Professor in Forest Tree Genetics, Genomics and Biotechnology College of Forest Resources and Environmental Science Michigan Technological University Phone: 906-487-1835

On Wed, May 1, 2024 at 12:04 AM James Ferguson @.***> wrote:

Hello,

squigglePlot can take slow5/blow5 files directly

In the help of the script under "-w", "--slow5",

James

— Reply to this email directly, view it on GitHub https://github.com/Psy-Fer/SquiggleKit/issues/65#issuecomment-2087943450, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUXV2772UQ75DZTFYXP4EWLZABSWXAVCNFSM6AAAAABHBMUJT6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBXHE2DGNBVGA . You are receiving this because you authored the thread.Message ID: @.***>

yinyuanmtu commented 5 months ago

Hi James, Just let you know that with blow5 files, the squigglePlot worked perfectly. Thanks for all the help! Yinan

Yinan Yuan, PhD Assistant Professor in Forest Tree Genetics, Genomics and Biotechnology College of Forest Resources and Environmental Science Michigan Technological University Phone: 906-487-1835

On Wed, May 1, 2024 at 12:04 AM James Ferguson @.***> wrote:

Hello,

squigglePlot can take slow5/blow5 files directly

In the help of the script under "-w", "--slow5",

James

— Reply to this email directly, view it on GitHub https://github.com/Psy-Fer/SquiggleKit/issues/65#issuecomment-2087943450, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUXV2772UQ75DZTFYXP4EWLZABSWXAVCNFSM6AAAAABHBMUJT6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBXHE2DGNBVGA . You are receiving this because you authored the thread.Message ID: @.***>

Psy-Fer commented 5 months ago

Great to hear.

Let me know if you need anything 🤓

James