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I'm having issues in mapping gene names in Seurat objects from droplet datasets to ENSEMBL IDs.
For example, in `droplet_Bladder_seurat_tiss.Robj` there are 2887 gene symbols that could not be mapp…
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Hi there,
Thanks for making this tool - there's definitely a need for a consistent framework for calling pseudogenes across disparate prokaryotes, and this seems like a great method to do that.
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Hi, thank you for this useful tool.
Is it possible to use RAST annotation output file?
Best regards,
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Hello,
Working with a set of _Salmonella_ genome annotations downloaded from NCBI Assembly, I stumbled upon the following problem at the GFF parsing step of Panaroo (v1.2.8, downloaded via Conda):
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I'm using AGAT to remove isoforms from my annotation (and ultimately the protein fasta) for OrthoFinder. My small pipeline:
1. checks the number of genes and mRNA in the original .gff
2. runs agat…
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Is it possible to annotate the pseudogenes out using database? For example, i want to know what is the most possible function genes the pseudogenes originally is.
ylifc updated
2 years ago
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Hey all!
Thank you for the pseudofinder package! I wanted to ask a few questions regarding pseudofinder for shotgun metagenomes (read length-150bps)
A) If I run the pseudogenefinder using the defa…
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Hello
I wonder about the Interpretation of "complete (pseudogene)" in nlr.txt output.
I understand that the gene have all the essential NLR motifs.
How the NLR annotator detects that this gene is…
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Hello,
I'm interested in using the pseudogene detection on some gene calls that have already been made in Prodigal. Is that possible? When I run Prokka independently, the gene calls don't match my …
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Hi pagoo,
love the program. was working great when using prokka annotations, however, I just tried to redo an analysis with bakta annotations and when creating the running the panaroo_2_pagoo and …