[Bioc-devel] DEXseq for only ONE gene

Sindre Lee sindre.lee at medisin.uio.no
Sat Mar 11 17:42:28 CET 2017

I know that DEXseq may be used of exon-levels analyses.

However, I am only interested in ONE gene, because a novel exon is discovered in this gene, by other researches. There are one "old" known transcript using exon-1a and the rest of the gene, and this "new" transcript using exon-1b and the rest if the gene.

Now, I want to see if there is a different usage of exon-1a vs. exon-1b between lean and obese people.

My approach is:
1. Make a new custom GTF-annotation file with the novel exon. This GTF-file thus contains info about the "old" and the "new" transcript. Since it does not exists in any known repertoires yet.
2. Using tophat2, only provide chromosome 7 (where the gene is located) and this GTF as annotations.
3. Count the reads uniquely mapped exon-1a and exon-1b. And also sum all reads on the gene.
4. Normalize the exon expression to total gene expression and perhaps to library size?
5. Simply use linear regression i.e. exon~sum.of.reads+library.size+obese

Is this "valid"? Am I overlooking something major? I know I ignore some dispersion estimates etc. and that I ofc could run the whole DEXseq pipeline. But I want to save time and get intuitive answers. DEXseq is hard to understand and hard to explain to coworkers.


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