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2.7 years ago
Pegasus ▴ 80
I used spades for assembly of bacteria-Illumina reads, and galaxy-Prokka for annotation Visualization of the annotation results showed me:
Summary of the active entries: contigs: 65
1- how can I confirm that annotation results are correct? 2- I am confused, why there are no pseudogenes in my report!!
Thanks for your time
As far as I know, PROKKA does not give you pseudogenes in the genome. You should manually focus on pseudogenes, such as C, N-terminus missing fragmented on ORF. However, I do not know If there is another method to find pseudogenes in the genome.
Thanks ugurcabuk for the answer. I wonder if it's essential to find pseudogenes in order to publish a draft genome, and submit it into NCBI !!
Hi Seraph, I think, you can send an e-mail to NCBI submission portal (http://firstname.lastname@example.org) about it. By the way, I found something that can be useful. See the link.
I tried to use this tool, but as I am a beginner, I am still facing this problem; NCBI PGAP yami file
chmod +x. Or you can call it through