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Computation of cryptic transcript ratios between first and intermediate exons Exon counts were generated using the featureCounts function with parameters: isPairedEnd = TRUE, strandSpecific = 2, GTF.featureType = exon, GTF.attrType = transcript_id, GTF.attrType.extra = gene_id, allowMultiOverlap = TRUE and useMetaFeatures = FALSE and the same GTF as for gene counts