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Getting to differential isoform/transcript expression using featurecount #1893

Closed sr320 closed 6 months ago

sr320 commented 6 months ago

How do you eventually get to differential isoform/transcript expression in the Hisat -> FeatureCount workflow?

sr320 commented 6 months ago

quick chatGPT indicates

Quantification of Features: FeatureCounts is primarily used for gene-level quantification. For transcript/isoform quantification, a tool like StringTie or HTSeq might be more suitable. However, if gene-level quantification is acceptable, you can use FeatureCounts.

laurahspencer commented 6 months ago

I have not used featureCounts to get isoform counts. I'm tackling the alternative splicing question at the exon level, based on this study - Mehmood et al. 2020. I'm currently doing differential exon usage using STAR -> featureCounts -> DEXSeq and can report back once I have results.

sr320 commented 6 months ago

thanks