User: Lesley Sitter

gravatar for Lesley Sitter
Lesley Sitter540
Reputation:
540
Status:
Trusted
Location:
Netherlands
Website:
https://lesleysitter.com/
Last seen:
3 weeks, 3 days ago
Joined:
6 years 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


 

Posts by Lesley Sitter

<prev • 65 results • page 2 of 7 • next >
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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) ...
written 5.1 years ago by Lesley Sitter540
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Answer: A: explaining N50 to grand mother
... 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 5.1 years ago by Lesley Sitter540 • updated 11 months ago by RamRS30k
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
... 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 5.1 years ago by Lesley Sitter540 • updated 4 months ago by RamRS30k
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Comment: C: How Can I Count Snps In My Vcf Files?
... 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  ...
written 5.1 years ago by Lesley Sitter540
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Comment: C: Extracting column value from csv file according to if else and & operator
... It also is a duplicate question, see post; 156628 (https://www.biostars.org/p/156628/) ...
written 5.1 years ago by Lesley Sitter540
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Answer: A: Extracting value from csv file with condition using if else and & operator
... 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 5.1 years ago by Lesley Sitter540
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Comment: C: VCF_format, a point in REF/ALT columns
... You should probably create a separate post for you question otherwise people won't find your question and won't be able to answer. ...
written 5.1 years ago by Lesley Sitter540
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Answer: A: Nice open source alternative to "contig viewer" in SeqMan Pro
... 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 5.2 years ago by Lesley Sitter540
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Answer: A: probability of mapping a random string of four nucleotides in a genome
... 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 5.2 years ago by Lesley Sitter540
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Answer: A: kmergenie keeps suggesting the highest kmer in range as the suitable one (?)
... 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 5.2 years ago by Lesley Sitter540

Latest awards to Lesley Sitter

Scholar 11 weeks ago, created an answer that has been accepted. For A: How does MAKER decide which proteins go into the final output?
Teacher 11 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
Epic Question 17 months ago, created a question with more than 10,000 views. For A:orthomcl with local mysql server on linux server, complete install
Scholar 17 months ago, created an answer that has been accepted. For A: How does MAKER decide which proteins go into the final output?
Appreciated 3.8 years ago, created a post with more than 5 votes. For A:orthomcl with local mysql server on linux server, complete install
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Removing contigs with improbable coverage using R?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Optimal minimum read length PE HiSeq reads for denovo assembly
Scholar 3.8 years ago, created an answer that has been accepted. For A: Maker annotation failure
Great Question 4.0 years ago, created a question with more than 5,000 views. For A:orthomcl with local mysql server on linux server, complete install
Appreciated 4.4 years ago, created a post with more than 5 votes. For A:orthomcl with local mysql server on linux server, complete install
Popular Question 4.8 years ago, created a question with more than 1,000 views. For A:orthomcl with local mysql server on linux server, complete install
Teacher 5.1 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
Scholar 5.2 years ago, created an answer that has been accepted. For A: Maker annotation failure
Teacher 5.2 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
Scholar 5.3 years ago, created an answer that has been accepted. For A: Maker annotation failure
Scholar 5.3 years ago, created an answer that has been accepted. For A: Maker annotation failure
Autobiographer 5.4 years ago, has more than 80 characters in the information field of the user's profile.
Popular Question 5.7 years ago, created a question with more than 1,000 views. For A:orthomcl with local mysql server on linux server, complete install

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