Missing pseudogenes in annotation report

Question

[Pegasus]

Hi all,

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

bases: 5736331

CDS: 5102

gene: 5279

misc_RNA: 52

rRNA: 9

tRNA: 115

tmRNA: 1

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

[young_bioinformatician]

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.

[Pegasus]

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 !!

[young_bioinformatician]

Hi Seraph, I think, you can send an e-mail to NCBI submission portal (http://[e-mail]) about it. By the way, I found something that can be useful. See the link.

PGAP

[Pegasus]

Hi ugurcabuk

I tried to use this tool, but as I am a beginner, I am still facing this problem; NCBI PGAP yami file

[young_bioinformatician]

1. please, make sure the file is executable. If not, you can do it using chmod +x. Or you can call it through python pgap.py.
2. some descriptions about yaml file is on the tool's github page, wiki section. See the link. Input-files