Shareef Dabdoub

Possibly related, while running DRAM-v annotate: ``` 2023-05-09 15:23:36,625 - Getting hits from dbCAN lib/python3.10/site-packages/mag_annotator/database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this GT2_Glycos_transf_2 look like an id...

I would suggest using [kraken-biom](https://github.com/smdabdoub/kraken-biom) to convert your output report files to a BIOM table, then import into [phyloseq](https://joey711.github.io/phyloseq/) where you can [filter based on taxa](https://joey711.github.io/phyloseq/preprocess.html#preprocessing): ` GP.chl = subset_taxa(GlobalPatterns,...

Hi! I'm glad the library has been useful to you! Thank you for the reminder. I finally got some time to get back to this and added a few long-standing...

Hi Rick, thanks for the question! From what I've read in the new manual, it should work with the v2 report output. However, I haven't had a chance to build...

Hi Camila, I have not yet created a kraken2 database for myself yet, so I don't have any example files to test it with. But I would be happy to...

Hi MaryoHg, The counts recorded in the biom table are counts assigned to a particular taxonomy ID (column 3 in the report file), with one exception. When assigning reads for...

@kyoreth Do you have an example file I could take a look at? I haven't actually tested kraken-biom with Bracken output. Others have said it works, but it would be...

Hi Paul, Apologies for the delay in responding. It looks like the issue is changes between Kraken and Kraken 2. The original Kraken used to report a '-' for anything...

Hi Martin, Apologies for the delay in responding. Example files would definitely help here. Shareef

@camilagazolla Thank you! I've had less time to work on this than I would have liked, but it's coming.