Mix paired end and single ends sequence in the same analysis


I am comparing different dataset of 16S rRNA, I wondering if I can mix paired end and sigle end datasets in the same analysis.
Thanks in advance

Hello! I do not think you can do that in mothur as mothur needs 2 strands to make error corrections.

If it is really what you need to do, I think your only option is Dada2.

Best of success.

Hi Lia -

Regardless of what software you’re using or how you treat the sequencing errors, I think mixing single and paired end read data is a bad idea. The data will have very different error profiles. I’d encourage you to analyze the datasets separately to test your hypothesis and then see if the results agree and go from there.