[Biojava-l] jRe: using phred calls with ChromatogramGraphic produced from ab1 files

[Andrew Farmer]

Eric-
thanks very much for your insights, the phred -c trick might in fact be 
exactly what I need. If not, I will check out the other code you have 
sent and follow up off-list if I have further questions.


Andrew


Eric Haugen wrote:
> 
> Hi Andrew,
> 
> It looks like what I did three years ago was turn off the 
> ChromatogramGraphic's call boxes:
> 
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_SEPARATORS, 
> Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER, 
> Boolean.FALSE );
> 
> then set the range based on the chromat positions in the phred file:
> 
> graphic.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE, 
> startIndex );
> graphic.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, endIndex );
> 
> and finally just draw Phred's base calls myself based on the chromat 
> position scale.
> 
> I don't know if you'll find it useful, but I've attached 
> PhdSequence.java and support code which I use as an alternative to 
> PhredSequence currently in biojava, which I think ignores chromat 
> positions.
> 
> But the easiest solution may be to have "phred -c" convert your ABI 
> chromats to SCF files containing the phred base calls.
> 
> -- 
> Eric Haugen
> Software Engineer
> University of Washington Genome Center
> ehaugen at u.washington.edu
> (206) 616-7582
> 
> On Thu, 13 Mar 2008, Andrew Farmer wrote:
> 
>> 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
>> adf at ncgr.org
>> (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
>> ---
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>

-- 

Andrew Farmer
adf at ncgr.org
(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
---