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[email protected] committed Jan 13, 2025
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Expand Up @@ -206,7 +206,7 @@ Allele-specific, gene-level differential expression analysis is then performed u


"allelic-whatshap"
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**allelic-whatshap** mode applies a standard alignment to a nonmasked genome with STAR, followed by allele-specific splitting
of mapped files with whatshap, requiring a phased vcf file as input ( ``--phased-vcf`` ). Gene-level quantification is performed for each allele using **featureCounts**.
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