terrimporter / co1classifier Goto Github PK

Dear Dr. Porter,

I've been trying to retrain the RDPClassifier to be used for a custom database on CO1; and starting from your trained dataset as a baseline I've moved towards retraining using just my custom data. I've realised that I'm currently missing any documentation regarding the construction of the "gene_copynumber" file that should be used in the last steps of retraining the classifier. Is there any documentation available on the topic?

Thanks in advance,
Marco

Would it be possible to add Homo sapiens COI seqs in the following releases? Would be very useful to detect human "contamination"

Hi, I'm trying to re-format the training data to have 7 consistent taxonomy levels (Kindgom, Phylum, Class, Order, Family, Genus, Species), but I'm unsure how to parse the "mytaxon.txt" file or FASTA headers into a format that I can easily manipulate them in R.

Essentially, I want to use your database with the RDP classifier included with the DADA2 pipeline, but I need to reformat the sequence names to have this format.

Any thoughts or suggestions would be greatly appreciated, and thanks for all your work putting this reference DB together.

Hey guys,

I wanted to use your train dataset (V4) to taxonomically assign my sequences in dada2 using the RDP classifier. I am a bit confused though on how to actually do this with the files provided in the trained tar.gz directory.

I have unzipped the CO1v4_trained.tar.gz but there is no fasta file with reference sequences. Isn't that what is needed as input for the RDP classifier? The genus_wordConditionalProbList.txt file is a pretty large file so I am pretty sure this one is being used for the actual taxonomic classification, I just don't know how exactly.

I have the feeling I totally misunderstand how your datasets are being used with the RDP classifier, sorry for that. Your help is much appreciated.

Cheers
Nauras

I was wondering if a newer version of your database is going to be made available anytime soon? The v4 seems to contain sequences only up until 2019?