No reads using demux on version 2019.10

[thermokarst]

@nnusbacher

Yes, I mentioned that I had first tried without the reverse complement flags and received the error that no sequences mapped to the samples

Yep! My point is that there are some questions you need to ask your sequencing center in order to get a handle on the data. The first thing to confirm is whether or not your barcodes are Golay barcodes (you mentioned in your post you used EMP barcodes, which should be Golay barcodes, but worth double-checking).

Please see these posts for discussion of the things that should get sorted out in the discussion with the sequencing center:

Clarification of a bug/or not a bug? qiime2 demux with little reads (2019.4 version to 2019.7 version)

Hi @ben! I think the parameter you are referring to is --p-no-golay-error-correction Nope, not a fluke, just poorly described. Let me try and summarize! Without Golay error correction, it doesn't matter the orientation your barcodes sequences are in, so long as they are the same orientation as the barcode mapping in your metadata file. If they aren't, you can use --p-rev-comp-barcodes to reverse complement the barcode sequences to match the barcode map OR use the --p-rev-comp-mapping…

Demuxing golay barcodes?

Woohoo! Because for non-Golay barcodes, the orientation doesn't matter, so long as the mapping barcodes are in the same orientation as the barcode sequences. The computer literally does a line-by-line check for equality: is AAAC equal to AAAG? No, then this sequence isn't from Sample 1. With Golay error correction, the orientation matters 100% --- the barcode sequences and the mapping sequence both need to be in the 5′ -> 3′ orientation in order for 1) the error correction to work…

Hope that helps.