Alignment and read quantification
The reads were aligned to the spike-in complemented Ensembl release 94 of the Homo sapiens assembly GRCh38 from the Genome Reference Consortium. The alignment was performed with the splice-aware aligner STAR version 2.6.1a. The alignments were quantified based on the annotations of Ensembl GRCh38.94 and the spike-in-specific annotations of Lexogen with the featureCounts software program version 1.6.4 of the subread analysis package.