Question: RNAseq read counts generated by FeatureCounts
0
23 days ago by

Hello I used FeatureCounts to do the read counts for my RNAseq data . Do the read counts FeatureCounts provide an average or absolute total of all the reads of the exons per gene ? Is there any way to get the read count for a specific exon in a gene?

rnaseq featurecounts • 66 views
modified 23 days ago by James W. MacDonald52k • written 23 days ago by adeler0010

Cross-posted: https://www.biostars.org/p/408898/

Answer: RNAseq read counts generated by FeatureCounts
2
23 days ago by
United States
James W. MacDonald52k wrote:

This is covered in the help page for featureCounts:

useMetaFeatures: logical indicating whether the read summarization
should be performed at the feature level (eg. exons) or
meta-feature level (eg. genes). If ‘TRUE’, features in the
annotation (each row is a feature) will be grouped into
meta-features, using their values in the ‘GeneID’ column in
the SAF-format annotation file or using the ‘GTF.attrType’
attribute in the GTF-format annotation file, and then reads
will be assiged to the meta-features instead of the features.
See below for more details.



And as mentioned, there are more details in the Details section.