Comments (2)
Hi Alex,
The ARTIC protocol is indeed brilliant. However, there have been some issues with two of the primer sites and this is discussed on line. It would be worth contacting ARTIC about this directly - there is also a preprint describing a potential fix.
With respect to running read until on these short amplicons we are currently limited to grabbing a very specific smallest amount of data due to the way MinKNOW itself functions. We are trying to get resources to look at this in a bit more detail but I suspect the primer issue I allude to above may be what you are seeing and fixing this would resolve your problem better than read until would.
Best
Matt
from readfish.
Hi Matt,
Yes, I saw the discussion about the primer issues - copying in the link to the preprint in case someone else stumbles over this entry: https://www.biorxiv.org/content/10.1101/2020.03.10.985150v1?rss=1
To confirm, what we observe is consistent with the described primer issues - we're currently sequencing one library where the problem occurs, and the thought crossed my mind that RU could be used on the ongoing run as an immediate fix ;-).
I am closing this now, thank you for responding so quickly!
Cheers,
Alex
from readfish.
Related Issues (20)
- readfish with just depletion? HOT 4
- Not being able to finish the tutorial/test HOT 6
- Provide additional TOML files which provide examples of host depletion and other use cases for readfish.
- location of readfish output HOT 4
- toml_live handling issue
- Depletion setting and unexpected behavior HOT 2
- Question about Readfish basecalling performance for messy samples HOT 6
- Playback issue HOT 14
- Problem communicating with basecaller after MinKnow update HOT 10
- Detect MinKNOW version and warn. HOT 1
- Circular Binary Segmentation HOT 3
- Having only one region in toml caused issue HOT 13
- chore: update github workflow actions HOT 1
- Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED HOT 4
- comparison between MinKNOW and Readfish HOT 4
- Error with flongle flow cell splitting HOT 6
- chore: update FAQ
- next release candidate checklist
- High count of no-barcode that map to my targets HOT 15
- Readfish is not running for Flongle Playback Data HOT 9
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