To make a comparison between a local strain of bacteria (for example E. coli) with the standard one (NCBI) in terms of genetic content using next-generation sequencing (NGS), what is the lowest number of bacterial samples that must be sequenced to get reliable results?
Thank you in advance for any help.
it depends on the question you want to answer. is it easy to get or hard ? and so on
Hi @Ahmed,
Does this mean you want to compare genomic sequence? Or just selected genes? Or maybe variants?
What is the question you want to answer?
Hi @ Eshraka,
Thanks for your help.
Samples are not hard to get, but the cost of sequencing is considered.
Hi @ Jan,
I appreciate your input.
Yes, the project's main aim is to compare genomic sequencing between two strains or populations. Would there be much difference in sample numbers if selected genes were compared?
Hi @Ahmed,
The most important question is - What would you like to see as a result? Or, what type of information are you trying to find out?
Hi @ Jan,
Thanks for your response. Trying to determine how a genomic sequence is different between two bacteria (same strain) isolated from different sources or cause different symptoms. In other words, trying to find out how genomic variants could be related to the cause of the bacterium.
If you want to analyze genomic variants and you have a reference genome (as you mentioned in the description), I would do at least two samples each (biological duplicates) to be sure the variant is something general and not specific (~unique) for the particular sample. This could give you a hint about what you're looking for.
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