skovaka
commented
2 years ago 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
sbabbbie
Hello,
I am a researcher working on enriching fungal pathogen genomes from mammal host tissues, which I have successfully done using your UNCALLED software in the past. However, after being forced to update MinKNOW and then updating UNCALLED so it would work with the newest version, UNCALLED has essentially stopped functioning.
In the .paf files, no reads are being kept even though I know there is target DNA in the sample, and mapping to the target afterward using minimap2 does show there are reads from the target. Additionally, although the .paf says that reads are being ejected, I don't see the characteristic "spike" in the read length distribution in MinKNOW at the length they say they are being ejected at. The size distribution is in fact identical to a run I performed without UNCALLED, suggesting to me that UNCALLED is simply not working or actually enriching for my target.
Do you have any guidance?
Thank you!