Turning transcript estimate to gene level estimates

Question

[halo22]

Hello All,

I've used the featureCounts program on my bam files to estimate the transcript counts(below is the code snippet).
Since a single gene can have multiple transcripts associated with it. What would be the best way to calculate a gene level estimate? Can adding gene specific transcript counts used as a gene level estimate?

   fcounts <- featureCounts("myTest.bam",
              annot.inbuilt='hg38',
              annot.ext = "Homo_sapiens.GRCh38.83.gtf",
              isGTFAnnotationFile = TRUE, isPairedEnd = TRUE,
              GTF.featureType="exon",GTF.attrType="gene_id",useMetaFeatures=TRUE)
      write.csv(fcounts$counts,file='counts.csv')

[h.mon]

Are you sure you estimated transcript counts? I don't use featureCounts usually, but seems to me this command will return gene counts.

Answer 1

[Devon Ryan]

You've quantified genes, not transcripts, so you already have the values you want.