Question: RNAseq read counts generated by FeatureCounts
0
gravatar for Adeler001
8 weeks 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 • 196 views
ADD COMMENTlink modified 4 weeks ago • written 8 weeks 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 8 weeks ago by genomax76k

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

ADD REPLYlink written 8 weeks ago by Adeler0010

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

ADD REPLYlink written 8 weeks ago by Kevin Blighe53k

ok thanks for the answer , I now understand

ADD REPLYlink written 8 weeks ago by Adeler0010

ok thank you for your replies genomax and kevin

ADD REPLYlink written 4 weeks ago by Adeler0010
1
gravatar for colin.kern
8 weeks ago by
colin.kern770
United States
colin.kern770 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 8 weeks ago by colin.kern770
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