Question: exon counting with featureCounts
0
gravatar for inah
2.4 years ago by
inah0
inah0 wrote:

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

rnaseq • 988 views
ADD COMMENTlink written 2.4 years ago by inah0

You should add "Rsubread" as a tag to your question, otherwise the Rsubread author might not be alerted to your question.

ADD REPLYlink written 2.4 years ago by Gordon Smyth39k
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