RNAseq read counts generated by FeatureCounts
1
0
Entering edit mode
17 months ago
Adeler001 • 0

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
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
ADD REPLY
0
Entering edit mode

ok thanks for the answer , I now understand

ADD REPLY
0
Entering edit mode

ok thank you for your replies genomax and kevin

ADD REPLY
1
Entering edit mode
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.

ADD COMMENT

Login before adding your answer.

Traffic: 2460 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6