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

[lizgehret]

Hi @Karthika,

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

@Karthika

Around 10 articles, the 7 articles sequences were 16S sequencing, and the rest of 3 articles were Whole Genome sequencing.

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.

@Karthika

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?

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