Thank you, everyone, for your answers. If I want to remove singleton from my data. How much removal of the singleton is acceptable? If I remove all the singletons is it acceptable?
Thank you, everyone, for your answers. If I want to remove singleton from my data. How much removal of the singleton is acceptable? If I remove all the singletons is it acceptable?
I think the basic idea is that you have a pool of data that has many instances of the same things. If you find one thing that is different from everything else, it was probably a mistake in the experimental process.
I think the basic idea is that you have a pool of data that has many instances of the same things. If you find one thing that is different from everything else, it was probably a mistake in the experimental process.
It is a gene/sequence which is absent from similar strains of the same species. Only one strain hosts it in the species/genus/pool being studied. Removal of such low-frequency sequences improves microbiota assessment by reducing error-rate.
It is a gene/sequence which is absent from similar strains of the same species. Only one strain hosts it in the species/genus/pool being studied. Removal of such low-frequency sequences improves microbiota assessment by reducing error-rate.
following
following
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Thank you, everyone, for your answers. If I want to remove singleton from my data. How much removal of the singleton is acceptable? If I remove all the singletons is it acceptable?
Thank you, everyone, for your answers. If I want to remove singleton from my data. How much removal of the singleton is acceptable? If I remove all the singletons is it acceptable?
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To simply put, a singleton means a sequence that cannot be matched to its counter strand.
Examples)
5'-ATGCAATTGAA-3'
3'-TACGTTAACTT-5'
These aligned pairs are correctly sequenced.
5'-ATGCAATTGAA-3'
3'-TNNANNAANN-5'
In this example, only one strand is sequenced, and the counter pair cannot be matched, so the sequence is a singleton.
Please refer to following pages:
https://drive5.com/usearch/manual/singletons.html
http://seqanswers.com/forums/showthread.php?t=46711
To simply put, a singleton means a sequence that cannot be matched to its counter strand.
Examples)
5'-ATGCAATTGAA-3'
3'-TACGTTAACTT-5'
These aligned pairs are correctly sequenced.
5'-ATGCAATTGAA-3'
3'-TNNANNAANN-5'
In this example, only one strand is sequenced, and the counter pair cannot be matched, so the sequence is a singleton.
Please refer to following pages:
https://drive5.com/usearch/manual/singletons.html
http://seqanswers.com/forums/showthread.php?t=46711
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following
following
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I think the basic idea is that you have a pool of data that has many instances of the same things. If you find one thing that is different from everything else, it was probably a mistake in the experimental process.
I think the basic idea is that you have a pool of data that has many instances of the same things. If you find one thing that is different from everything else, it was probably a mistake in the experimental process.
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It is a gene/sequence which is absent from similar strains of the same species. Only one strain hosts it in the species/genus/pool being studied.
Removal of such low-frequency sequences improves microbiota assessment by reducing error-rate.
It is a gene/sequence which is absent from similar strains of the same species. Only one strain hosts it in the species/genus/pool being studied.
Removal of such low-frequency sequences improves microbiota assessment by reducing error-rate.
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They refers to single reads, which can be removed from analysis.
They refers to single reads, which can be removed from analysis.
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A singleton is a OTU (Operational Taxonomical Unit) with only one sequence. They are removed to reduce sequencing errors.
A singleton is a OTU (Operational Taxonomical Unit) with only one sequence. They are removed to reduce sequencing errors.
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