Fixing high quality discrepancies with change to low quality

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dpaetkau
Posts: 29
Joined: Fri Jun 05, 2009 6:18 pm

Fixing high quality discrepancies with change to low quality

Post by dpaetkau » Thu Feb 21, 2013 4:04 am

Some of my students seem to have a problem. Here is one example of the problem:

When attempting to finish the project 1147E06 I found multiple unaligned high quality regions that were in fact bad sequences at the beginning or end of their respective reads. When I changed theses regions to low quality to the right or left they did not become resolved and still appear on the list of discrepancies. What should I do to fix this problem ?

When the students look at the problem area, it has been changed to low quality. When they quit Consed and go back to the area, it is still changed to low quality. So consed seems to be changing it to low quality. The unaligned high quality region does not disappear from the list of problems. Several students have this problem as their last issue before submitting. Any ideas?

wleung
Posts: 182
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Fixing high quality discrepancies with change to low qua

Post by wleung » Thu Feb 21, 2013 6:05 am

For highly repetitive projects, multiple unaligned high quality reads might indicate that the project contains a a misassembly. However, if examination of the unaligned high quality regions indicate that the discrepancies are in fact low quality, you can simply add a comment tag to indicate that you have reviewed that region and the consensus is correct. Consed will still report the region as unaligned high quality but we can examine the comment tag during the reconciliation process to verify that the region has been resolved.

To remove the region from the "Unaligned high quality" navigator, you will need to change the low quality bases to n's and then reassemble the project. Open the trace and navigate to the unaligned region, middle click on the first discrepant position and select "Change to n's to left / right". After editing the trace, you will need to reassemble the region using Miniassembly or reassemble the project using phredPhrap.

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