From: Alec W. <al...@br...> - 2012-12-12 22:41:28
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Hi James, We discussed this, and we think that what we're doing is better than what the spec indicates, so we're reluctant to change it. As I previously mentioned, if reads are clipped properly, this won't be an issue. -Alec On Dec 12, 2012, at 4:33 AM, James Bonfield wrote: > On Tue, Dec 11, 2012 at 11:38:22AM -0500, Alec Wysoker wrote: >> I'm not sure about the sign, but I think that in your example 99 is >> more likely to be correct than 101. For FR read pairs (i.e. not a >> jumping library), the two ends of the template are defined by the >> start position of the forward strand read and the end position of the >> reverse strand read. > > This was sort of my point. According to the spec they aren't > identified by the 5' and 3' ends, instead being identified by > left-most and right-most mapped base. > > I believe this was a change to the specification at some stage, but I > can't find my old copy now to verify that. > >> Given that the CIGARs seem wrong in these reads, my feeling is that >> FixMateInformation is setting TLEN to what seems intuitively right >> to me even though it does not agree with the spec. OTOH, I'm just a >> programmer and perhaps there is some molecular thing going on that >> I'm not aware of. > > I'm with you there, being just a programmer too. Most of the time it's > not possible to know what the correct answer is due to lack of > information. > > James > > -- > James Bonfield (jk...@sa...) | __---___---__ > | ~.._---___.."..___---_..~ > A Staden Package developer: | "--"" ""--" > https://sf.net/projects/staden/ | http://mobro.co/jamesbonfield > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. |