Search
Question: % of assigned reads using Rsubread featureCounts useMetaFeatures
0
gravatar for IV
8 months ago by
IV20
USA
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.

Anyone?

ADD COMMENTlink written 8 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 8 months ago by Wei Shi2.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 239 users visited in the last hour