3 months ago by
The fungi genome specific reads will fall out of the analysis during the mapping step to the plant genome.
Try using HISAT2 and set the output option to report unmapped reads to additional fastq outputs if you are interested in working with those later. That unmapped data will include both the fungi and any plant reads that didn't map, but you could map those against fungus genome(s) to filter.
The Galaxy RNA-seq tutorials cover HISAT2 usage in the context of an entire analysis, please see: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team