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Fixing low quality region

Posted: Thu Aug 30, 2018 4:01 pm
by dpaetkau
As a refresher to the students projects, I was working on the DBIA2377019 project.

It has one low consensus quality region that looks like this:
Screen Shot 2018-08-30 at 11.55.13 AM.png
Screen Shot 2018-08-30 at 11.55.13 AM.png (120.5 KiB) Viewed 6565 times
There are many illumina reads to back up a claim that the correct sequence should be:
CCCT G AAAAAAAAAA CAAAAAT
rather than the sequence from read DBIA2377019
CCCT A GAAAAAAAAA CAAAAAT

The new sequence with the change would look like this:
Screen Shot 2018-08-30 at 11.55.13 AM.png
Screen Shot 2018-08-30 at 11.55.13 AM.png (120.5 KiB) Viewed 6565 times
So, is there enough evidence to make this change. Adding new sequences is not going to fix the problem as there are already many illumina reads added.

Thank you in advance for your help.
Don

Re: Fixing low quality region

Posted: Fri Aug 31, 2018 3:19 pm
by wleung
Yes. There is sufficient supporting data from the Illumina reads to change the consensus.