[Bioc-sig-seq] GRanges, failure assigning chromosome lengths

[Sean Davis]

On Tue, Apr 27, 2010 at 10:51 AM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> Good morning Sean and everybody,
>
>>
>> Actually, the edge case is general as alignments, even on linear
>> chromosomes, may extend beyond the end of the chromosome, I believe.
>> In the best case, these alignments are clipped (in CIGAR terms), but I
>> don't know that all aligners are doing that appropriately.
>>
>> Sean
>
> So, you rather go for an overriding switch rather than infrastructure overhaul?
>
> I ask this because GRanges is an exceptionally convenient format for
> ChIP-seqers and Patrick is trying to make a decision to make it work
> for real world data.

I guess that I mean to say that the two issues of aligning off the end
of the chromosome and handling circular genomes are related but
separate issues.  An override seems quite reasonable for dealing with
the former.  Until aligners or common formats (BAM/SAM) deal with the
latter, it will be difficult to deal appropriately with circular
genomes, so an override is probably a fine compromise.

Sean


> And yes indeed: aligners do align a little bit past the boundaries
> even for linear chromosomes. Thanks for pointing that out!
>
> Ivan
>