Question: Flat file for functional annotation of draft fungal genome
gravatar for minions-b
2.0 years ago by
minions-b0 wrote:

Hi folks,

I am a wet-lab biologist with limited knowledge about scripting and programming. Now I am preparing a flat file for functional annotation of a draft fungal genome that I have deposited earlier at EMBL. I tried both gff3toembl and emblmygff3, but it seems they both do not like a draft genome. Do you know any scripts that work well with a draft genome with ca. 1000 contigs?

I am also thinking to deposit protein sequences instead of nucleotide sequence, but I am not sure if possible. Has anyone tried with protein sequences before?

All comments and suggestions are greatly appreciated!

ADD COMMENTlink written 2.0 years ago by minions-b0

I don’t get what could go wrong with those tools with draft genomes. The number of contigs doesn’t matter. The problem comes from something else. As I have been part of the development of Emblmygff3 I could help you with that one. Tell me what is the problem.

ADD REPLYlink written 2.0 years ago by Juke344.9k

Hi Juke-34, Thanks for your reply. I just discovered what could be wrong and it is actually a user-error. It is my first time trying to submit a draft genome.. :( Now I have split GFF3 for each scaffold and am trying to make a flat file for each scaffold individually using EMMLmygff3. Do you have any suggestion regarding what is the easiest way to make an EMBL flat file for those scaffolds without GFF3 annotation?

ADD REPLYlink written 2.0 years ago by minions-b0

I don’t get why you split the Gff file by scaffold It’s better/easier to keep all the contig’s annotations in one file. Is there any reason why you do that ? If for some contigs there is no annotation there will be annotation linked in the flat file that’s it.

ADD REPLYlink written 2.0 years ago by Juke344.9k
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