Following alignment (Hisat v2.2.1) of trimmed read pairs (cutadapt v2.7), and Gencode v38 feature quantification (featureCounts v2.0 in Rsubread package), alleles were phased using phaser.
For differential expression (DESeq2), count tables are processed via DESeq2_input_v03_TBLs_pass.R Analysis and plotting is performed via DESeq2_analysis_v04_TBLs_pass.R, which also calls AhernTBL_annotation_v01_pass.R to process additional annotations, and AE_analysis_v01_pass.R to call escapee genes.
Geneset enrichment analysis (GSEA) is performed via DESeq2_GSEA_TBLs_pass.R, and Weighted gene correlation network analysis (WGCNA) via WGCNA_DEG02_DTA_pass.R
For additional information please see the supplementary material at https://doi.org/10.1073/pnas.2211073119