Re: [Samtools-devel] Jumping Libraries and Split Reads

[Heng Li <lh...@sa...>]

On Tue, Jun 22, 2010 at 09:47:16AM +0800, Colin Hercus wrote:
> Hi Tim,
> 
> Thanks for the quick reply.
> 
> Thought of that one but I think it needs a large -ve number of N's,
> 68M-2000N32M

That is a problem because CIGAR disallows negative lengths. I do not
have a satisfactory solution. Perhaps I would store the split read in
two records and treat one part as single-end read. This is certainly not
optimal, though.

BTW, this is actually an example that arbitrarily defining orientation
in the @RG header is not always straightforward. When we have PacBio's
strobe reads, it will be even more difficult.

Heng

> 
> [image: Screenshot.png]
> Colin
> 
> On Tue, Jun 22, 2010 at 9:28 AM, Tim Fennell <tfe...@br...>wrote:
> 
> > I think I'd be tempted to represent this as one primary record per end,
> > with the split end having a large N operation in the middle of it's cigar.
> >  So if the junction turned up at base 70/101 I'd pull together the split
> > read alignment and generate a single cigar or 69M2000N32M.  The advantages I
> > see of doing it this way:
> >
> > 1) You still only have one sam record per end so all your usual inferences
> > apply
> > 2) All your bases from the one read are in one place
> > 3) You can actually count your split reads easily by asking how many reads
> > have jump-sized skips in them
> >
> > -t
> >
> > On Jun 21, 2010, at 9:22 PM, Colin Hercus wrote:
> >
> > > Hi,
> > >
> > > I'm not sure how how to represent paired end reads when one read has
> > split alignments and was wondering if someone could advise on the best
> > method.
> > >
> > > The issue arises with Illumina mate pair libraries where the junction
> > from cicularisation may land in one of the reads and result in a split
> > alignment for the read.
> > >
> > > SAM specifications allow two primary alignments for a split read and it
> > seems OK to use this to split one read but then we have the other read which
> > isn't split. To store two proper pairs with mate alignment locations, isize
> > etc. we need to store two alignments for the unsplit read. So what do we do
> > with the unsplit read, two records both primary or one primary and one
> > secondary but both with a primary mate?
> > >
> > > Any suggestions on how to represent this in SAM would be appreciated.
> > >
> > > Thanks, Colin
> > >
> > >
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