RNAseq read counts generated by FeatureCounts

Question

[Adeler001]

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?

[GenoMax]

They are actual read counts. You can remove the -g option which summarizes counts at gene level to get exon level counts.

[Adeler001]

genomax are the read counts a cumulative total or average of the read counts of the exons per gene

[Kevin Blighe]

Cross-posted: https://support.bioconductor.org/p/126561/

[Adeler001]

ok thanks for the answer , I now understand

[Adeler001]

ok thank you for your replies genomax and kevin

Answer 1

[colin.kern]

The read counts are not the average number per exon, they are close to the cumulative total, but not exactly because if a read spans a splice junction it would be counted as a read for two exons, but only contributes one count to the total gene count.