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tximport-workflow

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Import transcript-level quantifications from Salmon/kallisto/RSEM into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when summarizing transcript abundances to gene counts with the correct length offset, choosing a countsFromAbundance mode (full-length vs 3'-tag vs DTU), resolving transcript-ID version mismatches, or handing off to DESeq2/edgeR without double-applying the offset.

When to use

• Importing Salmon/kallisto/RSEM results
• Summarizing transcript abundances to gene counts
• Computing per-gene length offsets
• Choosing countsFromAbundance modes
• Resolving transcript-ID version mismatches
• Handing off to DESeq2/edgeR
• Transcript-level DTU analysis

When not to use

• 3'-tag protocols using length-scaled modes

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