Hi,
Just following up. I have tried to use cutadapt in qiime2 v2019.10 with combinatorial barcodes. I can confirm it is behaving the same way as reported in the previous thread: https://forum.qiime2.org/t/does-q2-cutadapt-support-dual-indexed-reads/11708/21. The result only demultiplexed samples with a first unique instance of the forward barcode, but ignored the rest. I have 130 samples, but only 16 samples demultiplexed.
At this time I do not believe the cutadapt plugin with latest version of qiime2 to be compatible with combinatorial dual barcodes.
Any suggestions other than making multiple metadata sheets, as suggested in the original post?
Thanks,
Amber
16S_c.tsv (25.7 KB) SampleData[PairedEndSequencesWithQuality]2.qza.qzv (296.1 KB)
####ran the following command to demultiplex
source activate qiime2-2019.10
qiime cutadapt demux-paired --i-seqs demux-paired-end2.qza --m-forward-barcodes-file 16S_c.tsv --m-forward-barcodes-column Forward_barcode --m-reverse-barcodes-file 16S_c.tsv --m-reverse-barcodes-column Reverse_barcode --o-untrimmed-sequences MultiplexedPairedEndBarcodeInSequence --o-per-sample-sequences SampleData[PairedEndSequencesWithQuality] --output-dir /global/home/hpc4605/Raw_data/Tick16sMiSeq2019/MiSeq_from_David/Out_Qiime_import/Demux_cutadapt_out/demux_cutadapt.qza
##confirm version
(qiime2-2019.10) [hpc4605@caclogin04 Out_Qiime_import]$ conda list | grep 'cutadapt'
cutadapt 2.6 py36h516909a_0 bioconda
q2-cutadapt 2019.10.0 py36_0 qiime2/label/r2019.10