Question: RNAseq read counts generated by FeatureCounts
0
gravatar for Adeler001
12 months ago by
Adeler0010
Adeler0010 wrote:

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 • 540 views
ADD COMMENTlink modified 11 months ago • written 12 months ago by Adeler0010

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

ADD REPLYlink written 12 months ago by genomax92k

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

ADD REPLYlink written 12 months ago by Adeler0010

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

ADD REPLYlink written 12 months ago by Kevin Blighe67k

ok thanks for the answer , I now understand

ADD REPLYlink written 12 months ago by Adeler0010

ok thank you for your replies genomax and kevin

ADD REPLYlink written 11 months ago by Adeler0010
1
gravatar for colin.kern
12 months ago by
colin.kern930
United States
colin.kern930 wrote:

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.

ADD COMMENTlink written 12 months ago by colin.kern930
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