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inah
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10
@inah-13176
Last seen 5.9 years ago
Hi,
I want to obtain read counts at the exon level using featureCounts. I run Rsubread and use these options:
annot.ext="/home/inah/RefGTF/GRCh38/annotation/Homo_sapiens.GRCh38.85.gtf",
isGTFAnnotationFile=TRUE,
GTF.featureType="exon", GTF.attrType="exon_id", useMetaFeatures=FALSE
The resulting count matrix has 1,182,163 rows but only 678,276 unique row identifiers, so there are multiple rows for the same exon-id.
Of course when I set useMetaFeatures=TRUE, then the resulting count matrix has 678,276 rows all with unique identifiers.
Sorry for the ignorant question, but why do I have so many more "exons" than "exon-ids"?
Thanks, Ina
You should add "Rsubread" as a tag to your question, otherwise the Rsubread author might not be alerted to your question.