How can I demultiplex and trimm after importing fastq file from Iontorrent

I have one fastq with 29 samples, only 6 of them are mine. It was used Ion torrent to sequencing. I used the fastq manifest to import the data to qiime 2 (Im using the 2020.2 version). And this .qza file have the barcodes and primers in it.
How do I take them out?
I have tied the cutadapt demux-single, but appears the error:

Invalid value for “–i-seqs”: Expected an artifact of at least type
MultiplexedSingleEndBarcodeInSequence. An artifact of type
SampleData[SequencesWithQuality] was provided.

Which makes sense I think. Any help?


Hello Alejandra,

Once you have imported your fastq files into a .qza file, you can use
qiime demux filter-samples
to keep just your 6 samples from the full data set.

But it looks like you have not got them imported just yet! The Fastq manifest format is for when you have samples in separate fastq files. Try importing using the cutadapt plugin:


Hi Colin, thank you for your response.

What I actually have is one file fastq with 29 samples. So yes I will try to import them with the cutadapt plugin that you mention! The file name is R_2019_11_13_19_51_37_user_SN2-93-Etchebehere_Vaz_AlejandraLatu_16S_Arquea_13_11_2019.fastq, and contains all the samples.

I understood that was the one that it worked for my type of data to import it.
Thanks again! Hope it work!!

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