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Prodigal penalizes predicting genes that are shorter than 250 bp (83 aa). As a result, Prokka is missing a number of short proteins that do exist in a closely related species. Any thoughts on how to d…
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Hi there!
I would like to validate experimentally some fused genes. For doing that, I should keep the most expressed isoform for each gene. I would like to know how FusionInspector decides the iso…
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Let's say someone ran the following command:
```
checkm2 predict --genes --threads 16 --database_path uniref100.KO.1.dmnd --output_directory checkm2_output --input genomes/ -x faa
```
In `c…
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relevant to #309
I've been working on annotating catlases. In this use case, I built a "metapangenome" graph. I did a genome query (_R. gnavus_) in 605 gut microbiome metagenomes, and then combined…
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I used HGTector2 to predict HGTs in my genome, and it classified my genome as "phylum Proteobacteria". The prediction results showed that 318 genes were identified as HGTs, but only 40 of them had a '…
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Hello,
In order to explore the regulons identified in my data with pySCENIC, I used the list of target genes for select regulons and analyzed them using iRegulon. However, after running the "Predic…
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Dear team,
Thanks a lot for providing scGPT for biological researchers. You provide a tutorial for perturbation prediction using Adamson or Norman's datasets. However, I am still confused about h…
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Got this error when trying to install prodigal
```
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mortonjt/Documents/micronota/m…
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I would like to know how AUGUSTUS treats masked regions on genome. I have a softmasked genome and I did a prediction on it, but I do not know if AUGUSTUS ignores these regions or predicts on them. If…
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Hi Gerry,
thank you for this very useful tool that accounts for the different confounding factors and errors when dealing with the comparison of gene sets between species and lineages.
I underst…