I have used Albacore (v2.3.3) to basecall my minION data locally on my machine. Within the produced "workspace" directory albacore is outputing two folders ("pass" and "fail") based on the qscore threshold set. However there are also 32 ".fast5" files that have not been placed in either of the "pass" or "fail" folders and are just sitting in the "workspace" folder. Does anyone know why these have not been placed in either the pass or fail folders? Has albacore just failed to move them to either "pass" or "fail" after basecalling? Is there another reason?
My summary file notes that a total of 247636 fast5 files were basecalled, however only 247604 total files are in the "pass" and "fail" folders. In other words, it seems the 32 spare .fast5 files have been basecalled, but for some reason left in the "workspace" directory.
Thanks!
Hi Ryan,
Unfortunately I don't have an answer to your question, but I would suggest to go to Nanopore community site (where you should have you profile if you bought the MinION) (https://community.nanoporetech.com/) and raise a new topic for discussion. Folks out there are pretty responsive and will probably be able to help you.
Deni
Hi Deni,
Thanks for the advice, I will likely create a post. I came here first because I find the Nanopore community site to be unnecessarily awkward and difficult considering the lack of the ability to search for topics/posts.
Cheers,
Ryan
Hi Ryan,
I would be great if you could keep this post updated once you have found the explanation for this behavior, e.g., in the Nanopore Community.
TIA.
Best,
Cedric
In general it decides based on the average q-score of the read. I think at the moment average_q > 7 is "pass", below is "fail".
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