Build Star Index for both Human and Pathogen Reference Genome

Question

[universe_life]

How to build a star index - consisting of both human and pathogen reference genome? At the moment I am downloading the human and pathogen GTF files from NCBI and for fasta sequences with respect to pathogen - I am merging the ones that I am interested in. I am then creating a STAR Index with respect to it. However in downstream analysis with respect to the star index generated - issues are coming up.

I would like to know the method by which you successfully built a star index using human and pathogen reference genome and steps for the same. Thank you.

[ATpoint]

That's the standard way. You should describe what did not work, and why. Just saying "does not work" is not helpful.