Reads were trimmed using cutadapt (40) and mapped to the human genome GRCh38 using STAR (41) v2.4.2a (with End To End option and out Filter Mismatch NoverLmax set to 0.04). Counting proceeded over genes annotated in Ensembl release 88, using an HTSeq count (42) (intersection-strict mode). Differential expression analysis was performed using DESeq2 (43) with the betaPrior, cooksCutoff, and independent Filtering parameters set to false. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg (44). The pipeline was constructed using Snakemake (45).

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