Hi all, my apologies if this is a silly question I am new to microbiome analysis,
I have completed my analysis using paired end reads (Illumina) with the 16s V3-V4 primer pair (341F - 805R) in QIIME (with DADA2) following this pipeline Amplicon SOP v2 (qiime2 2022.11) · LangilleLab/microbiome_helper Wiki · GitHub. I would now like to repeat this analysis but include sequences from another study to compare my groups.
This publication states that they also used paired end reads so I expected to download fastq files that contained the forward and reverse reads to include with my own sequences, then I can pass them both, together, through QIIME2 but when I downloaded these files it appears that the reads were already joined when submitted.
My questions are as follows:
- Do I need to split the joined reads from the publication into forward/reverse reads and then I continue with QIIME2?
- Or is it appropriate to pass the joined sequences as single end through the QIIME2, then merge the ASV tables from DADA2 for my study then proceed with normalization?
- Will treating treating one set as single end and another as paired end impact results? If so, is there a more appropriate method to complete this procedure?
Please feel free to share your expertise, thank you.