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Effects of the SCC-aware reference genome on common RNAseq analyses: (left) gene expression (Transcripts Per Kilobase Million; TPM) and (right) allele balance (allele-specific expression; ASE). For allele balance, we used the SCC-aware reference called VCF as a measure to increase the total number of transcripts included (see Table 3). Both analyses use the T2T-CHM13v2 genome sequence for mapping.
