How can I count one specific exon in RNA-seq data

Question

[carl.h]

I would like to quantify the number of exones of one particular exone in a specific gene. I have rnaseq data.

[GenoMax]

I assume you mean counts for a particular exon? Align to the genome/transcriptome as usual. Use a GTF containing just the data you are interested in for counting with featureCounts at exon level.

[carl.h]

Yes that is right. Thank you!

[carl.h]

For a follow up question, you don't happen to know how to count all exones in one gene? I have the gtf annotations for all the exones in one gene and I would like to get the number of each exon for the gene.

[GenoMax]

As long as you have the annotations in your GTF file you can count the exons separately (e.g. -t exon, which is the default for featureCounts. Take a look at the manual here.)

[carl.h]

Thank you it worked perfectly, I had to add -f to count feature.

Answer 1

[firatuyulur]

you can use DEXSeq on R see this.

Answer 2

[Charles Warden]

DEXSeq is a good suggestion.

If you wanted to use JunctionSeq for splicing analysis, QoRTs can provide exon and splice junction counts.