Hey,
I am an absolute beginner in metagenomics and maybe you can help.
After successfully completing metagenomic analysis of my samples and subsequent analysis of differential abundance of certain taxa, I would like to analyze to which bacterial strain the belong to.
Is it possible to chain StrainPhlAn to the output generated with nf-core/taxprofiler? After reading the StrainPhlan-documentation, I leanred that I need the SAM files (*.sam.bz2) generated by MetaPhlan for running StrainPhlan. However, when searching my results/ output-directory, I could not detect them. Is there -flagable options when running taxprofiler to have the SAM files (*.sam.bz2) saved?
Thank you for any advice!
Best,