I would like to quantify the number of exones of one particular exone in a specific gene. I have rnaseq data.
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.
Yes that is right. Thank you!
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.
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.)
Thank you it worked perfectly, I had to add -f to count feature.
you can use DEXSeq on R see this.
DEXSeq is a good suggestion.
If you wanted to use JunctionSeq for splicing analysis, QoRTs can provide exon and splice junction counts.
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