QIIME2 usage on both single-end and paired end sequences for Meta-analysis

Dear Experts,
I am new to QIIME2. I need to perform the Meta-data analysis work. For that purpose, I downloaded the files from NCBI using the Accession number. Around 10 articles, the 7 articles sequences were 16S sequencing, and the rest of 3 articles were Whole Genome sequencing. For that, I downloaded the SRA files. I got 2-SRA files as single-end sequence files and 8-SRA files as Paired-end sequence files. Is there any possibility to combine both Single-end sequences and Paired-end sequences into a single format, which will help for further analysis?
Or else, if I run the data by using single-end sequences related commands individually, likewise for the paired-end sequences and I get the data individually. That data can be analyzed further or not.
Kindly provide your thoughts and views to complete my meta-analysis work.

Thanks in advance.

Hi @Karthika,

Welcome to the :qiime2: forum!

I am about to sign off for the weekend, but I just wanted to let you know that I'll follow up with you first thing on Monday to help you out here!

Hi @Karthika,

Thanks for your patience here! Happy to address your questions below.

One cautionary point I'd like to bring up about this is that you'll only be able to utilize dada2 and/or deblur for denoising on your 16S samples (but not your WGS samples). Depending on what your analysis requires, this may or may not be relevant - but it's worth bringing up before moving forward.

You'll need to import, denoise, and demultiplex your single end and paired end reads separately - which will allow you to move forward in your analysis. Check out this forum post that addresses this same question in further detail (separating single end and paired end reads and any relevant comparisons between the two datasets).

Hope this helps!

Cheers :lizard:

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