Hi all-
I have been trying to use the ChromatogramGraphic class to display ABI
chromatogram data, whilst relating this to alignments of sequences
called from these trace files with phred. For example, if the user
clicks a putatively polymorphic base in an alignment viewer, to scroll
and highlight the region of the ChromatogramGraphic corresponding to the
ase call. However, I seem to be having some difficulty in establishing
correspondences between the phred base calls and the information shown
in the graphic.
As far as I understand what is being displayed by ChromatogramGraphic,
it is drawing "callboxes" around peaks corresponding to calls that are
stored by Chromatogram, which in turn is storing information about the
base calls that was encoded in the ABI file. These tend to differ
substantially (e.g. in lower-quality areas) from the calls made by
phred- e.g. an untrimmed phred-called sequence might have 1300 bases to
the abi-called version's 900 bases. So, I am trying to find some way to
get the ChromatogramGraphic callboxes to reflect the calls made by phred.
Has anyone else encountered this type of situation before? It appears
that phred's phd output encodes a trace offset for each of its calls, so
I would guess that one could conceivably overlay the phred calls into a
chromatogram produced by the abi parser in order to get the callboxes to
reflect phred's interpretation of the trace data.
I could be way off-base (no pun intended) in my interpretation, and
would appreciate any insights from the gurus out there. And if this is
more or less correct, and there is not yet a canned solution, any advice
on how to go about coding it in a way that could be contributed back to
the project would be great.
Thanks in advance
--
Andrew Farmer
[EMAIL PROTECTED]
(505) 995-4464
Database Administrator/Software Developer
National Center for Genome Resources
---
"To live in the presence of great truths and eternal laws,
to be led by permanent ideals-
that is what keeps a man patient when the world ignores him,
and calm and unspoiled when the world praises him."
-Balzac
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