Dear all, I have two question about orthorfinder software.
one question is that I have 3 species (A,B,C), each species select 4 timepoint for RNA sequencing. A and B species don't have reference genome, C species has a reference genome. Now, after all the analysis and differential expression analysis within each species, I want to find the genes exist in A,B species, but don't exist in C species, will orthofinder works for that?
Another question is that if orthofinder can help find that kind of genes, What will be the input file for orthofinder? My prediction is that for no-reference genome species A,B, after Trinity assembly to produce a fasta file, I can use TRANSDECODER to covert this fasta file to protein sequence file, then use the protein sequence as the input file for orthofinder. (But I also did the uniprot annotation, I am not sure if it is better to download the protein sequence from uniprot?)
I will be pretty appreciated if you could help with that or give me some suggestions!