Request for Raw Microbial Counts Data

[jiarui1120]

Hi！

I would like to express my sincere gratitude for your previous response. It was truly helpful and valuable to us.

Our previous expression may not have been very clear. The problem we are facing is that we need the raw microbial counts data for analysis. Hence, I'd like to inquire if this raw counts data is stored within the curatedMetagenomicData package. Also, I wonder if it would be possible for you to share this data with us for our research purposes.

Your assistance and consideration in this matter would be greatly appreciated. Thank you very much for your time and attention.

[lwaldron]

Dear @jiarui1120, there is some discussion of how MetaPhlAn3 estimates relative abundance here, and why it can't provide direct per-species counts - in short, because it does not use the majority of the genome that is shared between species, it uses only clade-specific marker genes which differ in length, number of genes per species, and copy number. We do also provide MetaPhlAn's estimate of those marker gene relative abundance output, which has undergone fewer steps of normalization than species relative abundance, so if you multiplied these by sequencing depth you would have something more closely resembling raw counts but you would have to replicate some of MetaPhlAn's calculations as simply adding those up per-species would introduce biases from the number of genes per species, copy number, and gene length.

There are some columns in sampleMetaData that may be relevant to you:

> sampleMetadata[1:5, c("NCBI_accession", "number_reads", "number_bases")]
  NCBI_accession number_reads number_bases
1     SRR4052021     27553455   2748531713
2     SRR4052022     32197545   3210606434
3     SRR4052033     32310216   3222955818
4     SRR4052038     14270590   1423299652
5     SRR4052039     37677351   3735487055