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Clipping Range parameter in GAP3 (Read 2108 times)
Feb 5th, 2021 at 1:35pm

joseluis   Offline
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I would like to know what the "Clipping range" parameter is for in GAP3. For example example, what does it mean a Clipping gange = 100? Thank you.
 
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Reply #1 - Feb 5th, 2021 at 4:01pm

Dmitrii Sukhomlinov   Offline
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Hello,

Have you seen the description?

Clipping range: One of the parameters to control clipping of a poor end region of a read (-y)

If there are quality values, CAP3 computes two positions qualpos5 and qualpos3 of read f such that the region of read f from position qualpos5 to position qualpos3 consists mostly of quality values greater than Quality cutoff for clipping.

If there are no quality values, then qualpos5 is set to 1 and qualpos3 is set the length of read f.

The range for the left clipping position of read f is from 1 to qualpos5 + Clipping range.
The range for the right clipping position of read f is from qualpos3 - Clipping range to the end of read f.
 

Best regards,
Dmitrii Sukhomlinov,
UGENE team.
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Reply #2 - Feb 6th, 2021 at 2:53pm

joseluis   Offline
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Sorry, I hadn't seen it. Thank you.
 
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Reply #3 - Feb 8th, 2021 at 1:38pm

joseluis   Offline
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I understand but by default the clipping range value is 100 and according to the definition if I apply this value then sort reads (about 200 pb) could dissapear, isn't it? Thank you.
 
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Reply #4 - Apr 2nd, 2021 at 10:52am

Bobby Rencher   Offline
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It looks a whole lot better to me.
 
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