Victor Solovyev (solovyev at sanger.ac.uk) wrote:
: We installed ABIQ - Read and View ABI trace file and potential
: Error positions
: ABIQ Program is prepared to analyze ABi trace files and calculate
: error probability for each base using a new version of the approach
: described in (Lawrence,Solovyev,1994).
: We plan to develop these tools further to use in sequence
: EDITING/ASSEMBLING and study of HUMAN POLYMORPHISM.
: If we observe different bases in several reads of some locus and
: these bases have very small probability of errors, than we have a
: good candidate of polymorphic site.
: The program compute the PROBABILITY OF 3 TYPES OF BASE CALLING ERRORS
: (Insertion - Overcall; deletion - Undercall and substitution - Miscall).
(snip)
: The sequence and probabilitoes of errors in 0-9 scale corresponding (0 -
: 100%).
It sounds very useful, but it would be a lot easier to spot the
non-zero probabilities if the program used "." instead of "0" for 0
probability.
For example:
: Example of output of the program:
: A01U0005 " View ABI traces and Quality data " (Java viewer button)
(snip)
: 360 370 380 390 400
: TAACCCAAACAGTGATCCTGGGGCTCCATTCCAGACCCAACTTAATCAGT
: P over 00000300000000000000000000000000000001000000000000
: P under 00020000000000000010000000000000000000000000000000
: P mis 00100400000000000000000000000000000002000000000000
: 410 420 430 440 450
: ATTTCTGGAGGTTGGACACTGACGGCTGTTATTTTTCAAAGGCATCCCAG
: P over 00000000000000000000000010000000000000000100000100
: P under 00002100011200000000011000000001000011000000020000
: P mis 00000001010000000000010000000000040000000100010200
: GGTGGA
: P over 000000
: P under 000000
: P mis 010000
would become:
360 370 380 390 4..
TAACCCAAACAGTGATCCTGGGGCTCCATTCCAGACCCAACTTAATCAGT
P over .....3...............................1............
P under ...2..............1...............................
P mis ..1..4...............................2............
410 420 430 440 450
ATTTCTGGAGGTTGGACACTGACGGCTGTTATTTTTCAAAGGCATCCCAG
P over ........................1................1.....1..
P under ....21...112.........11........1....11.......2....
P mis .......1.1...........1...........4.......1...1.2..
GGTGGA
P over ......
P under ......
P mis .1....
Best wishes,
--
Chris Boyd | from (but not \ MRC Human Genetics Unit
Christopher.Boyd at hgu.mrc.ac.uk | on behalf of) / Crewe Rd, Edinburgh
http://www.hgu.mrc.ac.uk/Users/Christopher.Boyd EH4 2XU, SCOTLAND
