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Question: K-mer counter tool should write k-mers occurring only once to the output file?
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gravatar for saranpons3
3.6 years ago by
saranpons3 • 70
saranpons3 • 70 wrote:

Dear Members,

I would like to know that Are k-mers whose occurrence is only 1(one) have any purpose in assembling/in any other Bioinformatics problem? A K-mer counter tool should write k-mers occurring only once to the output file?
kmer kmer counter • 1.2k views
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modified 3.6 years ago by Istvan Albert ♦♦ 86k • written 3.6 years ago by saranpons3 • 70
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gravatar for Istvan Albert
3.6 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

Since measurements are affected by random errors a kmer that was seen only once is typically considered to have originated from such an error. This reasoning usually holds - but of course, as always, there may be exceptions to it.

Which kmers are written to a file is an implementation detail - and may depend on the tool.
ADD COMMENT • link modified 3.6 years ago • written 3.6 years ago by Istvan Albert ♦♦ 86k

@Istvan Albert, Thanks for replying. Do you mean that K-mers which are occurring only once in the data set does not have any significance/purpose in assembling or any other bio-informatics problems?

ADD REPLY • link written 3.6 years ago by saranpons3 • 70

Due to redundancy a singleton k-mer in reads is likely a sequencing error. They could be significant post assembly though..

ADD REPLY • link written 3.6 years ago by 5heikki ♦ 9.3k

Thx 5heikki for your answer. It means can I say that generating singleton kmers is must by kmer counter tools.

ADD REPLY • link written 3.6 years ago by saranpons3 • 70
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