Question: Maker Output: transcript names
gravatar for mmacd
2.5 years ago by
United States
mmacd20 wrote:

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:



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!

maker annotation genome • 1.0k views
ADD COMMENTlink written 2.5 years ago by mmacd20

did you already get the answer for this?

ADD REPLYlink written 7 months ago by Vijay Lakhujani3.0k

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!

ADD REPLYlink written 7 months ago by mmacd20
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