Illumina V4 SE and V3 PE read merging and analysis

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:?: Hi all…

I have been searching forums and googling about my issue for the last few days with out any favorable leads, kindly clarify my doubts…

I had sequenced my samples using Illumina MiSeq platform for V3 paired ends. All samples belong to a single population. I need to compare my population with other populations that were previously studied, so, I went on to SRA and downloaded the required data. But the problem is all of them are V4 single end reads.

So, if I had to compare these two data-sets, whether I had to analyse them separately and compare just the results, or Is there a way to merge these 2 data-sets and analyse simultaneously?

I tried merging them using “Make.group” and “Merge.files”, but I got no output sequences after “align.seqs”. So, I analysed the two data sets separately till OTU classification. At this stage, both sets vary widely in OTU Ids. Is there a way to replace these OTU Ids and give some common Id in both the files, so that I can merge both the tables. Or shall I analyse separately…?

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Sorry, there’s a problem in jargon here. Are you sequencing the V4 region with the V3 chemistry or are you sequencing the V3 region?

If you are trying to compare the V3 and V4 regions, it will be pretty hard to make a comparison between the regions. You could try to classify them, but different regions classify differently and the primers each have their own biases.