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General Category >> Help and How-to >> Clipping Range parameter in GAP3 https://forum.ugene.net/forum/YaBB.pl?num=1612506946 Message started by joseluis on Feb 5th, 2021 at 1:35pm |
Title: Clipping Range parameter in GAP3 Post by joseluis on Feb 5th, 2021 at 1:35pm
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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Title: Re: Clipping Range parameter in GAP3 Post by Dmitrii Sukhomlinov on Feb 5th, 2021 at 4:01pm
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. |
Title: Re: Clipping Range parameter in GAP3 Post by joseluis on Feb 6th, 2021 at 2:53pm
Sorry, I hadn't seen it. Thank you.
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Title: Re: Clipping Range parameter in GAP3 Post by joseluis on Feb 8th, 2021 at 1:38pm
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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Title: Re: Clipping Range parameter in GAP3 Post by Bobby Rencher on Apr 2nd, 2021 at 10:52am
It looks a whole lot better to me.
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