First, cDNA FASTA files from the Ensembl archive were downloaded from both GRCh38 and GRCm38, with each transcript identified by a species-specific Ensembl transcript ID. The files were combined and run through kallisto index to build an index. Then kallisto quant was used to align each of the 5 pairs of mixed files to the combined index. The number of mouse sequences that matched to human species and vice versa in the resulting directories were counted using the R package Rsubread (Fig. 1).
