David Příhoda
David Příhoda
I guess you're mostly interested in training the BGC detection model on new BGC samples, right? So you can reuse the previous pfam2vec.csv file, it can be downloaded from here:...
@yangziyi1990 You can read our methods section to find how that was done. You'll need to run Pfam hmmscan on ~1000s of genomes to generate a training data corpus -...
Hi @drelo yes we are also using DeepBGC on metagenomic samples. Generally the longer your sequence, the better. You can use `--prodigal-meta-mode` to run Prodigal in '-p meta' mode to...
That sounds suspicious indeed. Can you try running deepbgc with the SPAdes `contigs.fa` file instead of the scaffolds file and adding the deepbgc `--prodigal-meta-mode` flag? If that still fails, it...
Great. What exactly do you mean by combining results?
Exactly, you can merge the TSV files (there's a BGC-level TSV and a protein domain-level TSV) or the genbank files. There's also a recent paper that introduces a method for...
BGCViz is relevant if you are also analysing your samples with other tools like antiSMASH.
Hi @chengyou96. Can you share the output of `deepbgc info`?
It looks like it didn't search in `conda-forge`, can you add that channel? It's a common one to have in your channels list alongside `bioconda` and `main`, a lot of...
That's a good point, I will keep that in mind, perhaps I could publish a short Medium article with a walkthrough. I think the biggest challenge here is finding a...