search

donia-lab / MetaBGC

A metagenomic strategy for harnessing the chemical repertoire of the human microbiome
GNU General Public License v3.0
32 stars 8 forks source link

Toy build for MetaBGC v1.3.3 #7

Closed deucy646 closed 4 years ago

deucy646 commented 4 years ago

I tried MetaBGC v1.3.3 with toy OxyN build from Google drive link. Some files are missing from the 'HiPer_spHMMs' folder of "OxyN" toy build. The missing files as stated by MetaBGC v1.3.3 as follows:

Can you provide the updated, suitable and complete toy build for MetaBGC v1.3.3. It would be a great help.

Junyu25 commented 4 years ago

Yeah, I meet the same problem. I think the Google drive build file they provide is for the old version of MetaBGC. I guess the problem is they didn't provide the true positive genes fasta file (only have a TPGenes.faa file, but what we need is the "Multi-FASTA with the nucleotide sequence of the true positive genes"), so we can't generate the <prot_family_name>_Scores.tsv or <prot_family_name>_FP_Reads.tsv file by the process. I think this method has a great potential, and I also want to adapt it to our project. So I hope @frcamacho @abiswas-odu you guys can provide the missing file for us to a demo.

abiswas-odu commented 4 years ago

The Google drive files are a small toy test for metabgc search. The method to to build a database requires creating a background of synthetic reads with the true positive genomes is described in the publication.