Demultiplexing error paired-end error

Hi there, I´m trying to demultiplex by following the paired-end read analysis protocol.

–m-barcodes-file sample-metadata.tsv
–m-barcodes-column BarcodeSequence
–i-seqs emp-paired-end-sequences.qza
–o-per-sample-sequences demux \

However I´m getting the following error:

"Plugin error from demux:

Mismatched sequence ids: D00420:191:HHG2GBCX2:2:1101:1916:2176, D00420:191:HHG2GBCX2:2:1101:12977:2149, and D00420:191:HHG2GBCX2:2:1101:12977:2149"

Any clues on what may be causing this?



Hi there @FranciscoC!

Please take a look at this post (and the rest of that thread) for more detail:

Can you tell us a bit more about your sequence data?

Thank you very much Thermokarst. I suspect that the problem is the same. I will also try to contact my sequence provider.

If this is the same issue I had, you could replace the N:0:1 to match across your forward, reverse, and barcode gzip/fastq files. The command would be to change the N:0:1 to match all.

The problem also occurred from our sequencing core where the forward would have the barcode N:0:1, but everything would be sequential (barcode file N:0:2) and reverse N:0:3.

A unix command to search and replace all N:0:2 and N:0:3 across the files to change to N:0:1 allowed me to import correctly. Of course, your problem may be different and before doing this, make a copy of everything and don’t use.

I’m at a different station, will provide the unix commands when I get back. Ben

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