Alex Predeus
Hello @nextgenusfs, Thank you for these comments on the installation! What makes it a bit harder and confusing for new users (like myself) is the fact that the instructions on...
Thank you for commenting - didn't notice that at all, I was just searching for comments that can bring some clarity to the instructions. I certainly didn't mean the comment...
Perhaps you need to softmask the genome? I've had a similar experience when my genome wasn't masked.
I have similar problem - I think perhaps "universe" definition is working in a way I don't understand? I've defined universe parameter to all protein-coding genes in my annotation (about...
Very nice to find this discussion. I was thinking about using vg to identify pseudogenes in cases when there are many finished sequenced genomes.
This seems to work now. Thank you very much! very convenient.
So, BUSCO v3 is the current version now. The links to v1 are all dead too. Any way to get around this?
Hello @markziemann , so I contacted Ensembl about the clarification. Apparently there's some sort of division that Ensembl does for its annotation; cDNA is meant to mostly include protein coding...
From my previous experience and discussions with other RNA-Seq bioinformaticians, Gencode seemed a bit better in terms of consistency and curation, while having a benefit of the same gene/transcript IDs...
If you are doing bacterial assembly, this is already done in Unicycler. For larger genomes, you're probably better off running something like MaSuRCa