[Bioc-devel] GenomicFeatures Introns
D.Strbenac at garvan.org.au
Wed May 25 08:00:31 CEST 2011
What do you think about RNA-seq reads over splice junctions ? Getting just the GRanges of the gap coordinates of each gapped read (from a GappedAlignments object), and overlapping them the gene introns list with type = "equal" using something like findOverlaps, would give you, for each possible splice junction of a gene, the number of reads that spliced across it ?
---- Original message ----
>Date: Wed, 11 May 2011 10:04:26 -0700
>From: Marc Carlson <mcarlson at fhcrc.org>
>Subject: Re: GenomicFeatures Introns
>To: D.Strbenac at garvan.org.au
>That is an interesting question with an interesting answer which I will
>attempt to describe.
>Our reasoning was that since introns are basically defined as the gaps
>between exons within a transcript, we were not sure whether it would
>ever really make sense to group them in another way. Basically I can
>easily imagine why someone would want to count all the exons for a gene
>or even why they might reduce something like that and then infer the
>resulting gaps as universally intronic sequence (for that gene). But
>that set of operations is NOT the same thing you would get if you
>counted starting with a potential intronsBy() method. In fact, if you
>had started with a naive intronsBy() method you might have horribly
>miscounted since you would have all sorts of exonic regions contained in
>some of your introns... :(
>But perhaps you have another idea of how to sort this out? If you have
>a compelling use case (and a way to do it that makes sense), please tell
>us about it on the biod-devel mailing list.
>On 05/11/2011 04:00 AM, Dario Strbenac wrote:
>> I have a short design question. In a wiki page
>> It has a intronsBy(txdb, by) function described, but in GenomicFeatures, there's a intronsByTranscript function. Is there a reason why the Wiki intronsBy options were dropped (which is more like how exonsBy currently works) ? I didn't ask on the list, in case there was an obvious reason.
>> - Dario.
Garvan Institute of Medical Research
Darlinghurst NSW 2010
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