Comments (4)
skovaka
commented on August 16, 2024
Very sorry for the trouble, I'm working on getting a sequencing run together so I can look into this. It is probably an issue with the new MinKNOW version. I recently tested the MinKNOW connection on an old flowcell (#44), but did not confirm that reads were being properly ejected.
I will hopefully be able to check on this within the next week, but in the meantime you could try using ReadFish, or MinKNOW's builtin "adaptive sampling" method
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sbabbbie
commented on August 16, 2024
Hello Sam,
Thank you so much for the quick response! I am also going to try out Uncalled on a sample I have run before and I know to have high amounts of the target DNA to confirm the replicability of the issue within the next few days, and will report back.
Looking forward to hearing back from you.
Spenser Babb-Biernacki
Pronouns: she/her/hers
PhD Student, Louisiana State University
***@***.*** | 623-210-3782
…________________________________
From: Sam Kovaka ***@***.***>
Sent: Thursday, June 23, 2022 1:15:42 PM
To: skovaka/UNCALLED ***@***.***>
Cc: Spenser Biernacki ***@***.***>; Author ***@***.***>
Subject: Re: [skovaka/UNCALLED] Updated Uncalled and Minknow No Longer Working (Issue #46)
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Very sorry for the trouble, I'm working on getting a sequencing run together so I can look into this. It is probably an issue with the new MinKNOW version. I recently tested the MinKNOW connection on an old flowcell (#44<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fskovaka%2FUNCALLED%2Fissues%2F44&data=05%7C01%7Csbiern1%40lsu.edu%7Cac21c9f532be42dfdb1d08da55446299%7C2d4dad3f50ae47d983a09ae2b1f466f8%7C0%7C0%7C637916049443576870%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2BVQGn%2BYke%2BCqzqTzkjJ%2Fj3mcp7VtyZWCqjuPsSqRVbM%3D&reserved=0>), but did not confirm that reads were being properly ejected.
I will hopefully be able to check on this within the next week, but in the meantime you could try using ReadFish<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FLooseLab%2Freadfish&data=05%7C01%7Csbiern1%40lsu.edu%7Cac21c9f532be42dfdb1d08da55446299%7C2d4dad3f50ae47d983a09ae2b1f466f8%7C0%7C0%7C637916049443576870%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=W6vY1Y0YxKvEG4IthYD6dYfqzHaL1Ik6sqPQXsuk0Yk%3D&reserved=0>, or MinKNOW's builtin "adaptive sampling" method
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skovaka
commented on August 16, 2024
Sorry for the delay, I have identified and fixed the main issue, which was related to signal calibration which MinKNOW used to perform but no longer does. Unfortunately, the ReadUntil API appears to be more finicky in general with the new update. I found that briefly running MinKNOW's builtin adaptive sampling fixes the problem. I've added a warning to the README which describes the problem and solution in more detail: https://github.com/skovaka/UNCALLED#real-time-readuntil
I know that's not an ideal solution, I will try to look into it further in the future.
Thanks,
Sam
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sbabbbie
commented on August 16, 2024
Hi Sam,
Thank you so much for taking the time to work on this issue. I’m out of town for the next week, but when I get back I will do a brief trial run to see if the issue is resolved.
Cheers,
Spenser
…________________________________
From: Sam Kovaka ***@***.***>
Sent: Thursday, July 7, 2022 2:18:11 PM
To: skovaka/UNCALLED ***@***.***>
Cc: Spenser Biernacki ***@***.***>; Author ***@***.***>
Subject: Re: [skovaka/UNCALLED] Updated Uncalled and Minknow No Longer Working (Issue #46)
You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Sorry for the delay, I have identified and fixed the main issue, which was related to signal calibration which MinKNOW used to perform but no longer does. Unfortunately, the ReadUntil API appears to be more finicky in general with the new update. I found that briefly running MinKNOW's builtin adaptive sampling fixes the problem. I've added a warning to the README which describes the problem and solution in more detail: https://github.com/skovaka/UNCALLED/edit/master/README.md#real-time-readuntil<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fskovaka%2FUNCALLED%2Fedit%2Fmaster%2FREADME.md%23real-time-readuntil&data=05%7C01%7Csbiern1%40lsu.edu%7Cb35f7d1023fe4330f71908da604d6f54%7C2d4dad3f50ae47d983a09ae2b1f466f8%7C0%7C0%7C637928182939868423%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=v0iWIcWB151Fd1VCeHvrFzNo79p3zU1Rm52LOTXPaMk%3D&reserved=0>
I know that's not an ideal solution, I will try to look into it further in the future.
Thanks,
Sam
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