Hi everyone, I am working with mouse stool samples and interested in exploring bacterial diversity. I have Mtx and MAGs from the stool samples, what would be the most appropriate reference for mapping metatranscriptomic (MTX) reads - MAGs or predicted genes from MAGs? or de novo assembly of Mtx reads would make sense?
Additionally, what Bowtie2 (pl suggest if some other method can work well) parameters would you recommend for mapping metatranscriptomic reads to MAGs or their predicted genes? Would you suggest allowing multimapping, considering the complexity and redundancy in microbial communities?
As I understand, mapping MTX reads directly to MAGs would provide abundance at the genome level, while mapping to genes predicted from MAGs would yield gene-level expression counts. Would I expect any significant difference if I were to aggregate gene-level counts back to their corresponding MAGs to compare with the MAG-level abundances?
Any suggestion would be greatly appreciated. Thanks :)
