Question: Is it advisable to include reference genome for pan-genome anlysis when working on specific type strains?
2
gravatar for ThulasiS
2.7 years ago by
ThulasiS60
ThulasiS60 wrote:

I constructed and analyzed pan-genome but now I got this doubt: Is it advisable to include reference genome for pan-genome analysis when working on specific type strains?

Please suggest me.

Thank you

pangenome genome • 526 views
ADD COMMENTlink modified 2.7 years ago by _r_am32k • written 2.7 years ago by ThulasiS60
2

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.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by _r_am32k

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.

ADD REPLYlink written 2.7 years ago by h.mon32k

Thank you Ram Sorry for my format

ADD REPLYlink written 2.7 years ago by ThulasiS60

Reference genome for whatever the reference strain is?

ADD REPLYlink written 2.7 years ago by Devon Ryan98k

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.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by ThulasiS60
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