Question: Maker Output: transcript names
0
gravatar for mmacd
2.7 years ago by
mmacd20
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:

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!

maker annotation genome • 1.1k views
ADD COMMENTlink written 2.7 years ago by mmacd20

did you already get the answer for this?

ADD REPLYlink written 10 months ago by Vijay Lakhujani3.4k

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 10 months ago by mmacd20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1060 users visited in the last hour