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
