% of assigned reads using Rsubread featureCounts useMetaFeatures
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IV ▴ 30
@iv-7340
Last seen 5.0 years ago
USA

I am testing the various featurecounts options from the very useful Rsubread package.

I have noticed that in all tested libraries (>100) using exon + useMetaFeatures (Ensemble gtf, GTF.featureType = "gene", GTF.attrType = "gene_id") assigns almost twice as many reads to features (metaFeatures) compared to exon without useMetaFeatures (all other settings are identical).

I know that the intent of feature and metaFeature read assignment is different but this vast difference puzzles me since the metafeatures are produced by combining the same exons.

I expected a reduction in assigned reads but the difference is quite large.

Anyone?

featurecounts rsubread • 1.2k views
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Hi @IV, I am not sure I understand your question. Could you please provide your code and also summary stat for each run?

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