Is there a in QIIME2

Hi all, long-time reader, first-time poster. Truth-be-told, I'm really not sure where to even post.

I have multiplexed data in three files: and R1, an R2, and barcodes. All three are in fastq format.

I need to submit to NCBI via SRA. The problem is that SRA requires individual index files for each sample, once they've been demultiplexed.

I use demux emp-paired to demultiplex. I realize that I can extract (i.e., qiime tools extract) the R1 and R2 fastq files, but I need the barcodes divided out by sample as well.

I could use QIIME and on the exported contents of my demuxed samples (the demux artifact produced by QIIME2), but I was wondering if QIIME2 had the equivalent?

Any help would be greatly appreciated.

Hello Joseph,

Welcome to the forums! :qiime2:

You have come to the right place.

Can you share the command you ran to demultiplex your reads? With that, we can find the barcodes.

Are you looking to remove the barcodes, or find them in order to add them to the metadata?

Hi Colin,

The command that I ran was,

qiime demux emp-paired
--m-barcodes-file Project_1/sample-metadata.tsv
--m-barcodes-column BarcodeSequence
--i-seqs Project_1/emp-paired-end-sequences.qza
--o-per-sample-sequences Project_1/demux.qza
--o-error-correction-details Project_1/demux-details.qza

Honestly, I'm not entirely sure what I am supposed to do with them. It looks like I'm just trying to extract them into another fastq file, while leaving them in the forward and reverse fastq files. However, I'm pressed for time, and cannot figure out the answer to that question for another couple of weeks (I'm in finals mode right now). Would it be okay to get back to you soon-ish on that second question?

I'm trying to automate a process for our lab right now. We had been using software provided by the sequencing lab that we use, but they only offer the software on PCs. I will actually have to compare the outputs to determine that.

I know, amateur hour, but I'm still learning!

The forum seems to have removed the space and backslashes from the ends of my commands.

Yes, you can follow up with me on your schedule. I'll see your message. :incoming_envelope:

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