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Hello,
I would like to confirm the Pseudogene annotation process. When giving as input a set of genes of interest that I'd like to check for pseudogenes, the pipeline checks wheter the input genes …
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Hi,
PGAP is an amazing tool! However, atleast for me sometimes its hard to understand the reasoning behind things. In MDS42: In an older annotation 2 neighboring CDS that were associated, were annota…
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Example when annotating Escherichia_coli_K_12_substr__MG1655_uid57779 genome:
```
NC_000913 257908 . G A . . .
```
You get an unexpected "intron" variant (since it's a bacteria you don'…
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Hi, thanks for this impressive piece of work. I'm running panaroo on a set of _E. coli_ genomes, which have been annotated by prokka with the exception of _E. coli_ K-12 (find the GFF [here](https://w…
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Need to change the default minscore to much higher than 100, approx 500? Validate this on a dataset of real sequences and pseudogenes.
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Hello,
First, I wanted to thank you for creating such a great tool, it has already proven to be very useful! However, when I run the annotate command, I get an error after the blastp/blastx search …
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Hi
I usually had no problems with the phobius step during annotation if I had run te predict and then annotation steps of funannotate
But now, in order to get a valid gbk file for existing NCBI …
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Hello,
I am using SnpEff for custom comparison of our in-house bacterial strains, and it's working very well so far. Making DBs is easy and smooth, and virtually all the info I need is generated i…
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We can give these different molecular function terms and /or products?
Would the driver poisons fit
GO:0090729 toxin activity
Molecular Function
Definition (GO:0090729 GONUTS page)
Inte…
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In #207, @fmarletaz asked me whether we have a way to add UTRs to transcripts derived from eg. Augustus. This made me realise that currently this is not the case, **not even in reference update mode**…