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evolgeniusteam / GMrepoProgrammableAccess

programmable access to GM repo
GNU General Public License v3.0
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relative abundance to counts #4

Open pameubillag opened 2 years ago

pameubillag commented 2 years ago

Hello, and thanks for your repository. I have been looking at the data, and I see that all abundances accessible are relative abundance. I haven't found any way to download counts data. Is count data available?? Also, as I am interested in count abundances, looking for a way to calculate it from relative abundance, I found a "nr_reads_sequenced," and I wonder what that number represents. For example, when it is metagenomic data, nr_reads_sequenced means all the oligonucleotides sequenced or bins?

evolgeniusteam commented 2 years ago

No, counts data are not available. Yes, you can obtain counts data using the relative abundances and the nr_reads_sequenced of the corresponding samples/runs. I have seen publications doing so. However, I never tried this and thus am in no position to judge whether it is a good or not.

The “Nr_reads_sequenced” always means the total number of sequencing reads in a sample/run, for both 16S and mNGS data.

Let me know if you need further assistance.

On Jan 13, 2022, at 06:32, Pamela Ubilla @. @.>> wrote:

Hello, and thanks for your repository. I have been looking at the data, and I see that all abundances accessible are relative abundance. I haven't found any way to download counts data. Is count data available?? Also, as I am interested in count abundances, looking for a way to calculate it from relative abundance, I found a "nr_reads_sequenced," and I wonder what that number represents. For example, when it is metagenomic data, nr_reads_sequenced means all the oligonucleotides sequenced or bins?

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pameubillag commented 2 years ago

Thanks for the clarification.