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mapping of Sanger reads - how to deal with insertions? (Read 1636 times)
Mar 15th, 2021 at 4:13am

Lennart   Offline
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Hello, I find the function to map Sanger sequencing reads to reference really great. The only problem I have is how to edit apparent insertions of an additional base caused by one read with low quality. I know I can use the edit function to remove the additional base from the low quality read, then do the same for the introduced '-' in reads showing the correct sequence. However, this procedure will also shift the consensus vs. reference by one base. Afterwards, scanning for additional ambiguous positions using the 'Jump to next variation' button will no longer work as most bases now will differ between consensus and reference.

I guess there is a more clever way to do this?

Thank you,
Lennart
 
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Reply #1 - Mar 15th, 2021 at 6:08pm

Dmitrii Sukhomlinov   Offline
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Russia

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I'm not sure that I get what you want. You can replace low-quality bases with gaps, for example, and consensus won't be shifted. Of what result do you want to have?

 

Best regards,
Dmitrii Sukhomlinov,
UGENE team.
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Reply #2 - Apr 13th, 2021 at 2:15am

Lennart   Offline
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Thank you for your reply. What I was looking for was the 'Remove all columns of gaps' function. Now it works  Smiley.
 
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