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catdesk / seqtrace

Automatically exported from code.google.com/p/seqtrace
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Can't work with files because of lack of quality data #6

Open catdesk opened 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/6

The .abi files given to me by my sequencing core do not contain quality data 
about the base calls. Consequently, seqtrace is reading the confidence of every 
call as '0', and will not let me edit the files or do anything because it 
requires a value for minimum confidence. If this could be changed to have an 
option to ignore quality data and allow me to still work with the sequences, 
that would be awesome. I like this program, but unfortunately I'm looking for 
alternatives because of this issue.

Tested on lubuntu 14.04 and windows 7 x64 with the latest version as of this 
post. 

Thanks.

Original issue reported on code.google.com by chillywi...@gmail.com on 20 Oct 2014 at 1:49

catdesk commented 8 years ago

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

Hello,

Thanks for your feedback!  Quality scores are so critical for most of 
SeqTrace's key functionality that, as you noted, they are a requirement for 
working with trace files in SeqTrace.

My recommendation in this situation is to use good base-calling software to add 
confidence scores to your trace files.  You probably ought to do this anyway, 
because quality scores are essential for ensuring that your finished sequences 
are reliable.  If you take a look at the FAQ page, you'll find detailed 
instructions for adding base calls to your trace files, including how to use 
the open-source base calling software TraceTuner: 
https://code.google.com/p/seqtrace/wiki/FAQ.

Original comment by stucky.b...@gmail.com on 29 Jan 2015 at 1:13