Dear Committee members,
Questions 1 - We assume that the reads from the taxa table are not the raw reads, are they? We couldn't find it in the documents how they were normalized and batch corrected.
Question 2 - Can we get the sequence associated with each ASVs identified with DADA2, please?
Thanks,
Yongchao
Created by Yongchao Huang yonghuang526 Hello @yonghuang526,
Question 1: The reads in the 'nreads' tables and in the long format (sv_long) are indeed the raw reads in the original specimens. There are also version normalized to relative abundance / fractional abundance from (0-1). We have left it to the participants to use whatever normalization technique (beyond relative abundance) they think is appropriate, or use methods (e.g. beta-binomial modeling) that use the raw read counts.
Question 2: We are unable to provide this information.
Tomiko on behalf of the 'Preterm Birth Prediction - Microbiome DREAM Challenge' team