Importing data, barcode read files missing

Hi there,

Having some issues importing data. My sequences were obtain from Mr DNA and I have a series of files, including the forward and reverse sequence reads. Examining the available examples, I believe that the most appropriate tutorial is the one that uses the EM protocol. I do not, however, have (or can find) the associated barcode reads files.

Any help would be greatly appreciated!



Hi @FranciscoC,

Sounds like you have already see our importing tutorials. It does not sound like you have EMP-formatted data, though. This is the main clue:

EMP format consists of only one forward, one reverse, and one barcode file.

It sounds like you have one forward and reverse read for each sample, indicating that your reads have already been demultiplexed. Check out the casava 1.8 format. If that does not work (e.g., your file names are not in the correct format), then you can use the manifest format described earlier in that tutorial to import just about any demultiplexed reads.

Let us know if that helps!

Dear Nicholas,

Thank you very much for answering back. I also have the fast, qual and mapping file, just like it was used in QIIME1. Any advice on how to proceed with this ones?

Again, many thanks.


A separate FASTA file and QUAL file?

Those will need to be merged into FASTQ prior to importing. QIIME 2 does not have any functions for doing this, because that is quite an old format. You can still use the functions in qiime1 to achieve this.

Yes, two separate files. Thank you very much. My problem with the casava or manifest format is that they were not demultiplexed, has I have several samples in my study and only two files.


Understood. I had misinterpreted this in your initial post.

I recommend you discuss this with the sequencing service — they should help you track down the barcodes.

Chances are the barcodes are located in-line in the sequence reads, in which case see this tutorial:

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