genome length and kmer size

How would an English person say this?

I am trying to glean meaning from this sentence, and I just cannot:

For a given kmer size, at what genome length will each k-mer occur once on average?

genome

• 1,786 views • link

written 6.9 years ago by M.O.L.S 10

Thanks, so: What is the genome length where each k-mer occurs just once if the kmer size = x. Thats a bit clearer.

• 0 views • link

written 6.9 years ago by M.O.L.S 10

This content does not belong in an answer. I have moved it to a comment, but it would seem like it belongs in the question (although I have no idea who you're thanking, given that no one else responded between when you asked the question and posted this "answer")

• 0 views • link

written 6.9 years ago by Ram 4.5K

someone responded and moved their response.

• 0 views • link

written 6.9 years ago by M.O.L.S 10

Hmmm this sounds like homework question rather than a real problem lol. But I think kmer's have 0 chance of repeating if the kmer size is equal to the genome size

• 0 views • link

written 6.9 years ago by biofalconch 132

I reached that conclusion too, but what's the formula you are using in general?

• 0 views • link

written 6.9 years ago by M.O.L.S 10

0 answers

No answers yet.

More posts like this

How to determine the K-mer size?
written 4.4 years ago by melissachua90 7

I have reads with 151bp length. I heard that the convention is to set the k-mer size as 1/2 to 2/3 the read length. In …
Why does kallisto indexing require odd-length k-mers?
written 6.4 years ago by ning 13

I was messing around with kallisto (v0.46.2). When specifying a k-mer length of 10 (*--kmer-size=10*), I got this error: > ```Error: k needs to be …
Genome Size Estimation
written 7.8 years ago by Mbillah 14

Recently I read a paper where they estimate their genome size by this formula: `G = k-mer number/k-mer depth` `Where, k-mer num=52 413 427 492, …
puzzled about "-kmer" options during de novo assembly
written 8.2 years ago by Yingzi Zhang 9

Hi all, I am puzzled about "-kmer" options during de novo assembly. **First**, I did k-mer frequency analysis. **Reported**: For P(x): Possible peaks including: 100 …
Guidelines to choose K-mer size for De bruijn graph based assembly (2nd generation sequencing reads…
written 9.0 years ago by saranpons3 7

Hello members, I would like to know that is there any guidelines to choose K-mer size for Debruijn graph based assembly (2nd generation sequencing reads). …
Running ABySS at k-mer > 97
written 9.1 years ago by Anand Rao 65

This post is related to, but different (a continuation) from my earlier post at https://www.biostars.org/p/268060/ seeking help with running the genome assembler software - ABySS. …
problem in estimatining BAC size using k-mer method
written 10.2 years ago by gangireddy 16

Hi people, I am trying to assemble BAC clone sequence from pacbio. The assemble using Celera Assembler and canu are both resulting one contig assembly …
Velvet: What's the relation between kmer coverage and normal coverage?
written 10.8 years ago by novice 115

I'm trying to convert the kmer coverage reported in the headers of my contigs into standard coverage. Velvet's manual says the relation between kmer coverage …
Build Graph lost k-mers
written 11.6 years ago by lardo 0

I have a FASTA file contains unique k-mers with the read length is the k-mer size: ``` >kmer_1 ATGACAGCCTTTTTTAAA >kmer_2 ATGACAGCCTTTTTTAAT ``` Then I used …
Can I Compile Velvet For K-Mer Of 201?
written 13.0 years ago by upendrakumar.devisetty 40

<p>I am trying to compile velvet to go a maximum k-mer length of "201" but velvet doesn't seem to respond to this. I am wondering …