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
