Hey!
I'm trying to learn some metatranscriptomics workflow, right now my approach is to run SortMeRNA to get rid of 16S RNA, the predict genes using FragGeneScanPlus. According to what I've been reading (https://www.frontiersin.org/articles/10.3389/fgene.2019.00904/full), the next step would be to identify each predicted protein fragment for which I was thinking about HMMER. Apparently, after this, I would be able to analyse differential expression in different sample groups but for this I would need a count table. Am I right expecting HMMER to give counts of each predicted transcript or should I run some other tool in the middle?. I went through the very well written HMMER manual (http://eddylab.org/software/hmmer/Userguide.pdf) but don't seem to find an answer to this.
Thanks a looot!
