How to demultiplex paired-end illumine reads with in-line barcodes?

[Nicholas_Bokulich]

Hi @hotblast,

@hotblast

Is there a better to demultiplex inline barcoded PE reads?

Take a look at cutadapt demux-paired. Based on your description, it sounds like this might be the plugin for you (unless if you are using dual-indexing, in which case see below) and will sidestep the need to use qiime1.

However, that probably won't fix the error that you are running into... here are my thoughts:

@hotblast

My last step is to demultiplex using “qiime demux emp-paired --m-barcodes-category BarcodeSequence”. There is no error message, but only <100 reads parsed out.

Based on your description, everything sounds correct so your low demux yields make me think of one detail in particular:

How do these barcodes in the barcode file compare to the mapping file? You may want to try adding the --p-rev-comp-barcodes parameter to see if that improves things.

It also sounds like you may be using a dual-indexing scheme, in which case this thread might also be useful to you.