Is it advisable to include reference genome for pan-genome anlysis when working on specific type strains?
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Reference genome for whatever the reference strain is?
I didn't get you Devon Ryan. But I'll explain here my concerns. I used Roary pipeline to construct pan-genome. I am anlyzing livestock associated strains but I have reference strain from human origin. So I was thinking if we include reference strain for pangenome size calculation, the size maybe varies. I tried with and without including ref strain but there is not much variation in core genome size. Since it is core. But I was little worried for reviewers questions while presenting the data. So, I was little confused.
Your question content is in the title and your body is "Look at the title"? Not a great way to structure your post :-)
I'd recommend moving the content to the body of your post (which I've done for you) and creating an appropriate title to summarize your problem.
I would go even further: add the info from your comment to Devon to the body of the question, but also explain how you did the analyses.
Thank you Ram Sorry for my format