Hi folks! so I do have a question: I work with a number of metagenomic samples - in-water microbial mats - we have DNA, mRNA, totalRNA sequenced. So, I've assembled DNA sequencing data, which resulted in contigs, and currently using Prodigal to predict ORFs from these. After blasting translated ORFs (I've used blastp on translated ORFs vs NR for efficiency), as expected, a number of predicted ORFs hit eukaryotes and archaeans. And I am a bit concerned if in this case I am doing things right by not segregating contigs before running Prodigal, that might be not the best option for ORF prediction for Eukaryota and Archean. Should I embed a segregation routine in the pipeline before calling Prodigal (what it should look like?), or should I simply re-call ORFs on contigs that hit eukaryotes with a Eukaryota ORF predictor?
