Hi everyone, Just a quick question. I am learning how to annotate genomes using maker (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018).

As a test, I downloaded Chromosome 2 of the fish Cottoperca gobio in fasta format, downloaded from NCBI here (https://www.ncbi.nlm.nih.gov/assembly/GCF_900634415.1). I managed to run maker and output the proteins from maker with the command:

gffread yourgenome.maker.all.gff -y yourgenome.pep.fasta -g yourgenome.sequence.fasta

I am checking the goodness of my assembly by comparing my .gff file with the .gff from NCBI using JBrowse and noticed that my maker run has one peptide sequence per one gene. In other words, for each gene in my chromosome I have only one protein, and I do not have proteins from alternative splicing (that are to be expected in a normal vertebrate genomes). So I was wondering, how do I obtain these proteins from alternative splicing in my genome? Is maker only considering/creating one protein per gene on purpose?

Thanks for your help, Best regards Luca