Open HadrienG opened 6 years ago
At least 10 datasets I think. Abundance level / Sequencing instrument: all the options provided by ISS :-) Do we want mixed datasets only? Or should we try some bacteria only, viruses only, etc. as well?
At least 10 datasets I think.
Completely agree. Depending on the db size and the power we need we could go up to a hundred. But I think 10 is a great start
Abundance level / Sequencing instrument: all the options provided by ISS :-)
Abundance level might be a bad word choice. I meant amount of species in the datasets.
Do we want mixed datasets only? Or should we try some bacteria only, viruses only, etc. as well?
I don't see what non-mixed datasets brings to the experiment. Am I missing something obvious? 😄
Amount of species: from 10 to 100 maybe?
For the non-mixed datasets, no I do not think that they bring anything. Just asking, because if I remember correctly they were easier to produce (if we do not provide the genomes, bu with the NCBI random option). But we do all mixed, that sounds good.
For the amount of species I'm on the opinion that we should stick to 1 to 3 different numbers, which would give us a design such as:
either we decide on fixed numbers for the diversities or we decide on ranges for the bins that will be needed for analysing the results.
Concerning the mixed / not-mixed questions yes not-mixed would be easier to produce with iss create --ncbi
but I doubt we will end up producing from random genomes from the ncbi, rather than from random genomes drawn from a selected sub-database as discussed in #3
I like this idea of the 3 different types. Fixed numbers or ranges: I do not know what is best. I guess it does not really matter.
Agreed for the second point, we will most likely not use the ncbi option
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