Read mapping statistics

[snayfach]

• [x] obtain data from Bryan
• [x] load into mysql
• [x] select metagenomes and viromes
• [ ] classify virus presence/absence
• [ ] quantify virus prevalence; metagenomes (overall, per region), viromes
• [ ] quantify virus abundance

[snayfach]

Emailed to Bryan

From your xlsx spreadsheet, there are a number of samples in the "metagenome_reads" sheet that are missing from "mg_metadata_Table_S4". One example is "Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317". Overall, there are 2798 rows in "metagenome_reads" and 1801 rows in "mg_metadata_Table_S4".

Response

Additionally, the second table ("mg_metadata_Table_S4") was generated by Matt Carter, who subset the original "metagenome_reads" table to provide one set of reads per individual, as many samples in "mg_metadata_Table_S4" come from the same individual. I believe he also did some quality filtering as well, excluding some samples with too low read depth, etc. He's out of town right now but I've asked him if he has the original table with all of the subject-level metadata prior to subsetting down to the 1801 rows.

Solution Only use the metagenomes containing metadata

[snayfach]

• Abundance statistics to consider
  • RPKM
  • % total reads
  • % viral reads
  • % viral genomes detected
  • % viral and bacterial genomes
• Geographic country preference (y / n)
• Geographic entropy
• Data type preference (virome / bulk)

[snayfach]

Analyses

• ultra prevalent viruses absent from viromes