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normalizing transcript-level expression data

Bioinformatics Asked on January 30, 2021

Generally, RNA-seq analysis tools like edgeR or DESeq2 work on gene-level data. For differential expression (or differential transcript usage), transcript-level data has its own caveats. However, for just visualization, is it reasonable to normalize transcript-level counts with classical methods (like TMM) or just stick with TPMs (generated by kallisto/salmon)?

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