demux for fastq files that don't have barcode in them?

Hey!
I am new to qiime so I am sorry if the answer is obvious.
I have data in the following format:

forward.fastq.gz
reverse.fastq.gz
barcodes.fastq.gz
metadata.tsv

I have used the EMP protocol to import the data in the following way:

qiime tools import \
  --type EMPPairedEndSequences \
  --input-path emp-paired-end-sequences \
  --output-path emp-paired-end-sequences.qza

The command went through successfully, my issue is that the follow up command:

qiime cutadapt demux-paired

is for data that has the barcodes in the data ( --i-seqs ARTIFACT MultiplexedPairedEndBarcodeInSequence --- is the only artifact I found) and my data is not of that type.
My question is if after the import using the qiime cutadapt demux-paired is ok as the import "fixes" the data or I need to use a different command?
If I need to use a different command, what is it?
Thank you very much for your assistance
Nadav

Hi @nadavlisha,
It is alittle hard for me to decode because I dont have the error messages.

from what I understand qiime cutadapt demux-paired command doesn't seem to be what you are looking for. qiime cutadapt demux-paired is used for removing barcodes from within your sequence and demultiplixing.

It looks like from your data format that you do not have your barcodes in your reads. if that is the case I would recommend using: emp-paired: Demultiplex paired-end sequence data generated with the EMP protocol. — QIIME 2 2024.10.1 documentation

If you do have barcodes in sequence, I think you may have imported your data wrong, but we can circle back to that if its relvant.

hope that helps!

1 Like

That does help!
Now I have a different question (it’s not from due to an error but about the arguments in another command)
After I used the qiime demux emp-paired command on my data I want to use the following command: qiime cutadapt trim-paired

however I don't know what should I put in the following arguments:
--p-front-f
--p-front-r
ext.
the command I used for single paired (qiime cutadapt trim-single) used the following string in the --p-front argument: GCTACGGGGGG

what should I put in the arguments?
appreciate the help
Nadav

Hi @nadavlisha,
The cutadapt plugin is designed for removing barcodes and adapters from your data. Do you have these in your data?

If not, I would suggest dada2 as your next action. I would also suggest the moving pictures tutorial “Moving Pictures” tutorial — QIIME 2 2024.10.1 documentation as a templete for common "initial" microbiome proccessing steps!

If you do have adapters in sequnces you will need to know the adapters that are in your sequence. I would recommend reaching out to the sequencer or the person who handed you the data to figure out what adapter sequence to remove.