Mixed Transcriptome Pipeline
STAR (v2.4.1d) aligns RNA-Seq reads to the reference genome of the first species of interest, then takes the unaligned reads and aligns them to the reference genome of the second species of interest. Post-alignment QA/QC is performed on both alignments. The default settings are used for both STAR alignments. This pipeline can be run on any Unaligned or Trimmed reads data node. You will need to add the reference genomes and build STAR 2.4.1d aligner indexes for the two species of interest. Please see our documentation for more information on how to add library files. This pipeline is useful for in silico separation of mixed transcriptome samples encountered when studying host-pathogen systems, xenograft models or symbiotic organisms.