Using ITSxpres with rescript and fit-classifier-naive-bayes

General Discussion
1

Hi!

I was thinking of using ITSxpres (instead of feature-classifier extract-reads) to extract the ITS2 region from the UNITE database. This is with the intention of making an ITS2 specific classifier. I am wondering about the wisdom of doing such a thing and any pitfalls.

thanks for any advice in advance,
Maurice

2

Hi @Maurice_Barrett ,
As far as I know, this will not work because ITSxpress operates on FASTQ data/prior to denoising, whereas the UNITE database is FASTA.

ITSx, the tool used in ITSxpress for extracting the ITS domain, is already what UNITE uses to extract the ITS domain in its standard database. So using the standard UNITE database will already give you what you are after, except that UNITE contains a mix of ITS1, ITS2, and full ITS.

So I think what you need is to figure out how to pull only those sequences that contain ITS2.

Good luck!

2 Likes