Hi, I work with an intracellular pathogen. I would like to run an RNA-Seq analysis in galaxy using a combined host-parasite transcriptome as reference and annotation (gtf) file. I expect about 2% of my reads are of pathogen origin and the remaining 98% of host origin. How do I create a combined host (pig) and pathogen (Cryptosporidium) references files with both species merged into one genome file and one annotation file?
Giovanni Widmer Tufts University