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catdesk / seqtrace

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Issue creating finished sequence #1

Closed catdesk closed 8 years ago

catdesk commented 8 years ago

Issue by GoogleCodeExporter Tuesday Mar 29, 2016 at 22:33 GMT Originally opened as https://github.com/catdesk/seqtrace-a/issues/1

What steps will reproduce the problem?

I have forward and reverse reads but the finished sequence is not being 
created. The sequences are aligning fine but there is no "finished sequence". I 
assume this is happening because there are no confidence scores. Apparently the 
chromatogram trace files do not include the scores, or they are no showing up. 
(I have attached an image)

Is it still possible to create a finished sequence? I tried to set the minimum 
confidence to 0, but that did not fix it. The program would freeze when 
generating the sequence.

What version of the product are you using? On what operating system?
Seq Trace 0.8, Windows 7.

Thanks.

Original issue reported on code.google.com by malcolmh...@gmail.com on 25 Feb 2013 at 3:45

Attachments:

catdesk commented 8 years ago

Comment by GoogleCodeExporter Tuesday Mar 29, 2016 at 22:33 GMT

I re-checked the version number, it should be 0.8.1, but in the "About" it 
still lists the program as 0.8.

Original comment by malcolmh...@gmail.com on 25 Feb 2013 at 3:51

catdesk commented 8 years ago

Comment by GoogleCodeExporter Tuesday Mar 29, 2016 at 22:33 GMT

I would like to use this software for a course, but the chromatograms I am 
using to test it must also be lacking confidence scores because I cannot get it 
to compute a working sequence. 

Was this issue ever resolved?

Thanks!

Original comment by kmkiem...@gmail.com on 2 Aug 2013 at 9:47

catdesk commented 8 years ago

Comment by GoogleCodeExporter Tuesday Mar 29, 2016 at 22:33 GMT

I have this problem too, downloaded version 0.8.1, but the "About" still show 
0.8.
There is no finished seq.
I use windows XP.

Is there anyway to make it work?

Thanks.

Original comment by kwc...@gmail.com on 3 Jan 2014 at 9:28

catdesk commented 8 years ago

Comment by GoogleCodeExporter Tuesday Mar 29, 2016 at 22:33 GMT

SeqTrace currently requires that the trace files it processes have quality 
scores for all of the base calls.  Most of SeqTrace's key sequence-processing 
algorithms require them.  Phred-type quality scores have been standard in DNA 
sequencing for quite a few years now, and they are essential for producing 
robust consensus sequences and high-quality single trace sequences.  All modern 
Sanger sequencing platforms use them.  Consequently, I have no immediate plans 
to implement support for trace files that lack base call quality scores.  
However, if you need to use such files, you do still have some options.

Sometimes, trace files without quality data have all zeros for the quality 
scores.  In those cases, you should still be able to export the raw base calls 
from SeqTrace.

Otherwise, you will need to add quality scores to the trace files before using 
them in SeqTrace.  Doing so is not particularly difficult.  If you have many 
trace files, the software program Phred is probably the easiest way to go.  If 
you have only a few, Nucleics online base calling software might be a good 
option (http://www.nucleics.com/peaktrace-sequencing/).  For more information, 
see the longer explanation I wrote for the FAQ 
(http://code.google.com/p/seqtrace/wiki/FAQ).

Also, I should mention that if you want to use SeqTrace for educational 
purposes and simply need trace files with quality scores, check out the NCBI 
Trace Archive: http://www.ncbi.nlm.nih.gov/Traces/trace.cgi.  There you will 
find literally millions of trace files that you can search by gene, organism, 
etc., and all of the trace files I have ever seen from the archive have quality 
score data.

I appreciate the feedback, and I'm sorry that SeqTrace doesn't quite do what 
you need.  I hope that some of the options above might be an acceptable way 
forward.

Original comment by stucky.b...@gmail.com on 19 Jan 2014 at 1:03