I am currently working on a Chironomus genome draft and want to do some gene annotation. It's the first time I am doing this and I wanted to use the maker pipeline but I am struggling with how to use it correctly.
I wanted to use the pipeline with GeneMark and Augustus to have 2 different predictions (also maker uses SNAP too by default?). Now I read I have to train Augustus for it to work but I struggle to do so. The Augustus website states I need data in GeneBank format which I am to obtain from EST alignments running PASA (another pipeline? outputting only in GFF3, not gb format?)
On the other hand I read that you have to run MAKER 2 times, once with genemark and snap and then again with Augustus added, but you have to train snap somehow (also it wasnt stated in how far this helps with my problem training Augustus)? I read the snap README and it states you are advised to contact the author of snap for help with training, but I am still waiting for a response.
Could someone experienced with Maker and Augustus give me some guidance? What is the best method to get this to work from scratch when I have the draft genome assembly and some RNAseq data / transcriptome data in fasta format to work with?
thanks in advance