Question: Differentiating between Constitutively spliced and Alternatively spliced exons
gravatar for dally
5.0 years ago by
United States
dally190 wrote:

Hey guys,

So this is kind of just a curious question. I was wondering what software and methodology is out there and if it's possible to take a reference genome of say hg38 for instance (from UCSC ?) And first ... give me a database or file of all the alternatively spliced exons (isoforms) ... and then differentiate whether an exon isoform is constitutive or alternative. 

I'm aware the question is rather vague, but it's really just a thought and I don't have any real questions behind this. Just wondering if it's more of a "gotta create your own custom script" or if there's some tools out there to do this and is thereby possible for someone with little programming knowledge.

ADD COMMENTlink modified 5.0 years ago by Devon Ryan97k • written 5.0 years ago by dally190
gravatar for Devon Ryan
5.0 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

Depending on how exact you want to be with your definition of an exon you might be able to do this with cut and uniq. I suspect, though, that this would be reasonably doable in R with GenomicRanges (load the GTF file, split by gene, pass that into a function that (1) makes disjoint intervals, (2) counts the intersects of them with the original GRanges object and (3) returns those ranges with more than 1 count).

Obviously the results of this are limited by the quality and completeness of the annotation, so don't read excessively into the results.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Devon Ryan97k
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