Problems editing bases

[GoogleCodeExporter]

Hello,

  I am running SeqTrace 0.9.0 using Ubuntu Linux v 13.1.0. I am using SeqTrace to view and edit ABI sequencer chromatogram files. However, every time I try to edit sequences, the menu buttons at the top of the sequence editing window are grayed out as are the editing options under the 'Edit' pull down menu. This happens when I open single or batch chromatogram files.  

  The sequencer machine used is an ABI 3130XL running KB Basecaller software v 1.4.0.

Any help you can provide will be greatly appreciated!

Thanks,
George

Original issue reported on code.google.com by [email protected] on 26 May 2014 at 2:08

[GoogleCodeExporter]

Hi, George,

Thanks for trying out SeqTrace and sending this issue report.

Just to make sure -- are you first using the mouse to select the bases you wish 
to edit (from the working/consensus sequence at the bottom of the trace view 
window)?  The editing controls will remain grayed out until one or more bases 
are selected.

Thanks,
Brian

Original comment by [email protected] on 28 May 2014 at 6:47

[GoogleCodeExporter]

I think that I´m with the same problem.

Original comment by [email protected] on 5 Aug 2014 at 7:58

Attachments:

• seq.png

[GoogleCodeExporter]

Dear Brian

now I understand how to use, I need select the base, not only click on.

Original comment by [email protected] on 5 Aug 2014 at 8:10

[GoogleCodeExporter]

I believe it should be easier to edit the sequences, because having to open and 
select an option for exchange takes too long. The rest of the software is great

Original comment by [email protected] on 5 Aug 2014 at 8:17

[GoogleCodeExporter]

I'm having the same issue using lubuntu 14.04. Even when I select/highlight a 
base, I'm still not able to edit. However, all of my confidence scores are 0, 
and I think this is probably the cause. Is there any way I can fix the 
confidence scores or tell seqtrace to ignore it (if my sequencing core doesn't 
actually include it)?

Original comment by [email protected] on 13 Oct 2014 at 6:23

[GoogleCodeExporter]

I select the base but it is still grayed out

Original comment by [email protected] on 6 Jun 2015 at 11:49

Attachments:

• Imagen1.png

[stuckyb]

There appear to be two issues in the comments here. The first is that you must first select the bases you wish to edit, then click on "Modify selected bases" to edit them. One commenter suggested that editing could be easier; I agree, and I will consider that as an enhancement for a future release of the software.

The other issue is that SeqTrace requires trace files that have quality scores associated with the base calls and will not work properly with trace files that lack quality scores. Read the answer to this question in the FAQ to learn how to add quality scores to trace files that do not have them.