User: Lesley Sitter
Lesley Sitter • 550
- Reputation:
- 550
- Status:
- Trusted
- Location:
- Netherlands
- Website:
- https://lesleysitter.com/
- Last seen:
- 1 month ago
- Joined:
- 6 years, 4 months ago
- Email:
- l***********@hotmail.com
Ellow peeps, I'm Lesley.
I have a BASc in biochemistry and a MSc in bio-informatics, a PhD in computational biology (working with bacterial data) and have both wet and drylab experiments.
My interests in regards to bio-informatics lie in NGS data, genome assembly, genotyping, comparative genomics and marker detection as well as creating scientific illustrations
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Comment:
C: explaining N50 to grand mother
... The N50 is ordered from longest to shortest and is then the first "long" contig that passes the 50% mark, not the other way around as you mentioned. At least, that is the method used in general papers and even Wikipedia (and we all know that everything on Wikipedia is the absolute truth XD)
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written 5.5 years ago by
Lesley Sitter • 550
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... I would draw something to explain it.
Telling her that a genome is very large and that is is very hard to find out the 1:1 exact order. Therefore you sequence contigs (or genome fragments or something like that). These fragments are ordered from large to small. You then count up the large fragments ...
written 5.5 years ago by
Lesley Sitter • 550
• updated
15 months ago by
Ram ♦ 32k
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... How about writing a tool and being convinced it works perfectly, so you start testing it on a complete dataset instead of testing it first on a subset and finding out after it ran for an hour or so that you made a tiny mistake somewhere. Sooo much time wasted that I'll never get back :P ...
written 5.5 years ago by
Lesley Sitter • 550
• updated
9 months ago by
Ram ♦ 32k
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... You should post this as a separate question seeing as it has nothing to do with counting SNPs, and also you posted this as an answer which it isn't. I would suggest you post a new question, that works a lot better because this post already has 3 answers so most people will probably ignore it
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written 5.5 years ago by
Lesley Sitter • 550
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... It also is a duplicate question, see post; 156628 (https://www.biostars.org/p/156628/)
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written 5.5 years ago by
Lesley Sitter • 550
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... It seems this is a duplicate post ( https://www.biostars.org/p/156653/ ), you should probably remove one or the other :S
Also it's not really a bioinformatics question but more an R problem. But it seems you are not consistently using capital and small letters, you created a data.frame named c but ...
written 5.5 years ago by
Lesley Sitter • 550
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... You should probably create a separate post for you question otherwise people won't find your question and won't be able to answer.
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written 5.5 years ago by
Lesley Sitter • 550
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... Couldn't you use the Integrative Genome viewer (IGV)?
You can just index your assembly (or whatever it is that has your contigs). Then load that assembly as a "genome" (doesn't matter if it is not an actual reference genome).
Once it has loaded, just load the sam/bam file which holds the alignment d ...
written 5.5 years ago by
Lesley Sitter • 550
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... Hi,
I'm no statistician but the chance is probably very high;
4^4 = 256 so about a 1 in 256 chance to find the string back. So if you think in terms of kmer's if you take a kmer of 4 and then the chance of one of these kmers being your random string is 1 in 256. So it will probably be something ...
written 5.5 years ago by
Lesley Sitter • 550
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... I have used KmerGenie a number of times on HiSeq Paired End reads and it's not that weird that the kmer is high.
KmerGenie takes a certain Kmer, for example it starts with 16, and looks at how many unique kmers it finds when doing that. Because the kmer is small the sequences obtained in that windo ...
written 5.6 years ago by
Lesley Sitter • 550
Latest awards to Lesley Sitter
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: probability of mapping a random string of four nucleotides in a genome
Scholar
7 months ago,
created an answer that has been accepted.
For A: How does MAKER decide which proteins go into the final output?
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: probability of mapping a random string of four nucleotides in a genome
Epic Question
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created a question with more than 10,000 views.
For A:orthomcl with local mysql server on linux server, complete install
Scholar
22 months ago,
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For A: How does MAKER decide which proteins go into the final output?
Appreciated
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For A:orthomcl with local mysql server on linux server, complete install
Popular Question
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created a question with more than 1,000 views.
For Removing contigs with improbable coverage using R?
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created a question with more than 1,000 views.
For Optimal minimum read length PE HiSeq reads for denovo assembly
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For A:orthomcl with local mysql server on linux server, complete install
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created a question with more than 1,000 views.
For A:orthomcl with local mysql server on linux server, complete install
Popular Question
5.1 years ago,
created a question with more than 1,000 views.
For Maker produces duplicate mRNA sequence with different AED score, what is up with that?
Teacher
5.5 years ago,
created an answer with at least 3 up-votes.
For A: probability of mapping a random string of four nucleotides in a genome
Teacher
5.5 years ago,
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For A: probability of mapping a random string of four nucleotides in a genome
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Popular Question
6.1 years ago,
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