RNAseq read counts generated by FeatureCounts
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17 months ago

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?

RNA-Seq FeatureCounts • 759 views
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They are actual read counts. You can remove the -g option which summarizes counts at gene level to get exon level counts.

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

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ok thanks for the answer , I now understand

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ok thank you for your replies genomax and kevin

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17 months ago
colin.kern ▴ 970

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.