I have a question about the output of Maker. After running fasta_merge on the Maker results, I get the fasta files which include all the gene annotations from all the different contigs in the assembly. In the transcript file, I get headers such as the two below:
I was wondering what this header means, for instance are 3.11 and 3.12 exons on the same gene or are they two completely separate genes? I ran maker was splice variants off, so there shouldn't be more than one transcript per gene (I am assuming if I run with splice variants on I would get mRNA-1 and mRNA-2 for the variants).
Thanks in advance!