How to remove primers and barcodes during denoising?

Dear Experts,

I have managed to import my demultiplexed data. Now I want to run data2 for denoising process but I am not sure whether my reads still contain primers and barcodes. I checked the study from which I collected my data to see which primers they used but there wasn't any information on that.

Here is a screenshot of one of my fastq files

If there are any primers or barcodes present in my reads what values should I used for --p- trim - left

Any help would be greatly appreciated.

Hi @ptalebic!

The best way to find out is to ask your sequencing center - they can provide guidance about what primers can be found in the reads, if any, and where they should be searched for.

Maybe! It depends on if those reads are on the 5' end, or the 3'. Let us know what you find out from your sequencing center.


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Dear Matthew,

I obtained my data from ENA - European Nucleotide Archive using an accession number provided in the paper I read and there is no information on the primer sequences in the paper.

Is it possible that they had all non-biological sequences removed prior to submission? I am asking this because the number of reads I have after importing my data into QIIME matches the number of reads they got after quality filtering as stated in the paper.

I see.

Iā€™m not sure - I am not involved with the curation of ENA (to the best of my knowledge, none of the QIIME 2 forum team is) - perhaps it would be best to check with ENA? Maybe they have submission guidelines that can help clarify things for you?

Maybe you could try contacting the original authors of the paper?

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