Maker Output: transcript names

Question

[mmacd]

Hi all,

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:

maker-Contig206-snap-gene-3.11-mRNA-1

maker-Contig206-snap-gene-3.12-mRNA-1

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!

[lakhujanivijay]

did you already get the answer for this?

[mmacd]

Hi Vijay, I had sent the same question to the Maker email list awhile back and go the following response:

"They are different genes because their ID’s are different. The numbers are meaningless, they are just iterators to make sure the ID’s are unique"

Hopefully this helps!