Closed ecastron closed 10 months ago
Hi Eduardo!
Yes, it is possible. If you have fasta files from those databases with the genomes that you're aligning against (compressed or uncompressed both work) then you can use mk_bowtie_index()
to compile a bowtie index from the folder of fasta files. Alternatively, you can make Rsubread indices with mk_subread_index()
if you want to use the subread aligner (but Bowtie 2 generally is more accurate). If you're having any trouble getting the databases to be compatible, let me know and I can take a look.
Brie
Hi Brie,
Thanks for the quick answer. That sounds great, I'd definitely give it a shot.
Eduardo
Hi @aubreyodom,
do you have any expericence with using sequence data from EnsemblBacteria? I've tried to use this database, but without any luck.
Cheers Bastian
Hi Bastian,
Sadly, I do not have experience with EnsemblBacteria. In the past, we've found that Silva is a good 16S database that is comparable to RefSeq's performance:
https://www.biorxiv.org/content/10.1101/2022.07.27.501757v1
The indices we used are linked on this page: https://github.com/aubreyodom/16SBenchmarking
Hi @aubreyodom ,
thanks for letting me know. I'll try Silva.
Cheers Bastian
Just an update for folks wanting to use another reference database - we are actively working on this issue and should have an update for metascope_id
in the coming months (if not sooner). I'm particularly interested in trying out Greengenes2 and Silva myself. Stay tuned.
Thanks @aubreyodom. Looking forward to trying it out!
@susheelbhanu A fix is now live on github (and should go live with the next Bioc release at the end of the month). Check out the db
and db_feature_table
parameters in the help docs, and let me know if you have any questions or specific cases. I'm going to go ahead and close this issue, but if something pops up feel free to reopen it.
Awesome, thank you 🙏!
Dear dev team,
Thanks for putting together an expanded version of pathoscope! I wanted to ask whether it was possible to use a database other than refseq. I usually work on environmental microbiomes and end up mapping against collections of metagenome-assembled genomes and/or the Genome Taxonomy Database (its taxonomy is the best; https://gtdb.ecogenomic.org).
Best,
Eduardo