Thanks Galt. I recognize that no example can completely defy misinterpretation, but I think it's worth trying to make them robust to common errors.
The most useful examples to me are the ones that I am least likely to be able to On Wed, May 2, 2012 at 12:25 PM, Galt Barber <[email protected]> wrote: > > Thanks for your reply. > We see your point. > Although not actually ambiguous, 4,26 is close to 5,27. > > We'll look into updating the FAQ. > I agree that revQEnd and revQStart > should be defined -- or that bit re-written > without undefined terms. > > -Galt Barber > UCSC BROWSER STAFF > > 4/1/2012 9:20 AM, Lucas Swanson: > >> Steve, >> >> You forgot about the extra 10 bases that Rhileigh added to the query >> length. i.e. qSize should be 41, not 31. >> >> 0 1 2 3 4 tens position in query >> 01234567890123456789012345678901234567890 ones position in query >> ++++ +++++ plus strand alignment on query >> -------- ---------- minus strand alignment on query >> >> >> So: >> >> qStart = qSize - revQEnd = 41 - 26 = 15 >> qEnd = qSize - revQStart = 41 - 4 = 37 >> >> >> Another issue with this equation in the FAQ is that "revQEnd" and >> "revQStart" are never actually defined. >> >> ~Lucas >> >> >> Steve Heitner wrote: >>> >>> Hello, Rhileigh. >>> >>> >>> >>> Your extension is incorrect. If we show the negative strand coordinates >>> of >>> the query, we would get: >>> >>> >>> >>> 0 1 2 3 tens position in query >>> >>> 0123456789012345678901234567890 ones position in query >>> >>> ++++ +++++ plus strand alignment on query >>> >>> -------- ---------- minus strand alignment on query >>> >>> 0987654321098765432109876543210 ones position in query NEG STRAND >>> coordinates >>> >>> 3 2 1 0 tens position in query NEG STRAND >>> coordinates >>> >>> >>> >>> Plus strand: >>> >>> qStart=12 >>> >>> qEnd=31 >>> >>> blockSizes=4,5 >>> >>> qStarts=12,26 >>> >>> >>> >>> Minus strand: >>> >>> qStart=4 >>> >>> qEnd=26 >>> >>> blockSizes=10,8 >>> >>> qStarts=5,19 >>> >>> >>> >>> The reason the negative strand qStart and qEnd are reported on the >>> positive >>> strand is because it makes very rapid searches for overlapping items >>> faster. >>> >>> >>> >>> If we do as the FAQ says, then in negative strand coordinates: >>> >>> qStart = qSize - revQEnd = 31 - 26 = 5 >>> >>> qEnd = qSize - revQStart = 31 - 4 = 27 >>> >>> >>> >>> Note that the blockSizes and qStarts are in negative-strand coordinates >>> and >>> the order of blocks in the list is reversed compared to the positive >>> strand. >>> >>> >>> >>> Please contact us again at [email protected] if you have any further >>> questions. >>> >>> >>> >>> --- >>> >>> Steve Heitner >>> >>> UCSC Genome Bioinformatics Group >>> >>> >>> >>> -----Original Message----- >>> From: [email protected] [mailto:[email protected]] On >>> Behalf Of Rhileigh Almgren >>> Sent: Monday, April 30, 2012 8:46 AM >>> To: [email protected] >>> Subject: [Genome] PSL format example >>> >>> >>> >>> Hi -- >>> >>> >>> >>> I would like to suggest an addition to the PSL format example given here: >>> >>> <http://genome.ucsc.edu/FAQ/FAQformat#format2> >>> http://genome.ucsc.edu/FAQ/FAQformat#format2 >>> >>> >>> >>> The current example is >>> >>> >>> >>> 0 1 2 3 tens position in query >>> >>> 0123456789012345678901234567890 ones position in query >>> >>> ++++ +++++ plus strand alignment on query >>> >>> -------- ---------- minus strand alignment on query >>> >>> >>> >>> Plus strand: >>> >>> qStart=12 >>> >>> qEnd=31 >>> >>> blockSizes=4,5 >>> >>> qStarts=12,26 >>> >>> >>> >>> Minus strand: >>> >>> qStart=4 >>> >>> qEnd=26 >>> >>> blockSizes=10,8 >>> >>> qStarts=5,19 >>> >>> >>> >>> To an ignoramus (me) trying to puzzle this out, the Minus strand qStart >>> and >>> qEnd values seem ambiguous. The stand is 30 bases long, so the >>> coordinates 4 >>> and 26 are not informative about the correct directional relationship. By >>> adding 10 bases to the query length, the ambiguity is resolved: >>> >>> >>> >>> 0 1 2 3 4 tens position in query >>> >>> 01234567890123456789012345678901234567890 ones position in query >>> >>> ++++ +++++ plus strand alignment on query >>> >>> -------- ---------- minus strand alignment on query >>> >>> >>> >>> Plus strand: >>> >>> qStart=12 >>> >>> qEnd=31 >>> >>> blockSizes=4,5 >>> >>> qStarts=12,26 >>> >>> >>> >>> Minus strand: >>> >>> qStart=4 >>> >>> qEnd=26 >>> >>> blockSizes=10,8 >>> >>> qStarts=15,29 >>> >>> >>> >>> Is my extension of the example correct? >>> >>> >>> >>> Thanks >>> >>> _______________________________________________ >>> >>> Genome maillist -<mailto:[email protected]> [email protected] >>> >>> <https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
