Question: % of assigned reads using Rsubread featureCounts useMetaFeatures
gravatar for IV
21 months ago by
IV20 wrote:

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.


ADD COMMENTlink written 21 months ago by IV20

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

ADD REPLYlink written 21 months ago by Wei Shi2.9k
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