User: Lesley Sitter

gravatar for Lesley Sitter
Lesley Sitter540
Reputation:
540
Status:
Trusted
Location:
Netherlands
Website:
https://lesleysitter.com/
Last seen:
1 month, 3 weeks ago
Joined:
6 years, 1 month 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 1 of 7 • next >
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Answer: A: Petition to demand that the Federal German Government release all genomic data o
... How is this different from having to pay fees to read articles that contain a large chunk of per-established information and often public data? Companies like Geneious asking $1000 licenses for a GUI around CC licensed publicly available tools that don't see a dime. People writing books containi ...
written 3 months ago by Lesley Sitter540
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Answer: A: problem with trimmomatic
... Heya, Potential reason for this error... Something could be wrong with your file paths, are you sure all the files are actually in the location from where you are trying to start the tool? It seems the error traces back to the Illumina clipper, so make sure 'adapters/TruSeq3-PE.fa' is the correct ...
written 3 months ago by Lesley Sitter540
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Answer: A: Best method for phylogeny on bacterial genes
... Several methods I've seen so far. Method 1: Gene array tree Concat all the genes into one sequence... this is an oldschool trick and only works for genes that have SNPs and one or two indels, but not genes that have vastly different sizes Method 2: Summary tree You can build individual trees for ...
written 3 months ago by Lesley Sitter540
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Comment: C: Roary producing erroneous plots?
... And when i convert the gene_abscence_prescence.csv to binary matrix, score the number of rows that have single entries. then count the number of rows per genome that belong to a orthologous group with only 1 entry... my plot looks nothing like this... so even the values it should represent based on ...
written 19 months ago by Lesley Sitter540
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Comment: C: Roary producing erroneous plots?
... For example, this is the default plot you get for New genes per genome... it's a whisker plot, meaning that each genome has a "range" of new genes... which is off course totally absurd unless there is some sort of "threshold" through which Roary analyzes these new genes (for example on a range of di ...
written 19 months ago by Lesley Sitter540
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Roary producing erroneous plots?
... Hi there, been using Roary for 3 years now... awesome tool! I'm just curious how it is that all the plots it produces aren't single values? For example... the "Number of unique genes" plot should just be a fixed single value of the number of unique genes am i right? So how come it's a collection of ...
R roary written 19 months ago by Lesley Sitter540 • updated 19 months ago by Joe18k
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Comment: C: A:orthomcl with local mysql server on linux server, complete install
... Hey Hudak7, sorry my project was over a year after the post so I kinda just left it to die (not much activity on it) I think it's a version control issue, when I used it there were some command that worked, that didn't seem to work anymore a year later. I'm very sorry but I won't be able to help you ...
written 2.6 years ago by Lesley Sitter540
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Answer: A: genome assembly software
... Keep in mind that most of the people here (bioinformaticians) are Linux based, and there is a good reason we stick to Linux for this type of stuff (windows based software are often unstable when dealing with this type of data sets).... BUT! DNA Star https://www.dnastar.com/ It's not my favorite bec ...
written 4.2 years ago by Lesley Sitter540
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Answer: A: Kmergenie k-mer estimate and multiple k-mers
... The graphs produced by K-mer genie are specificity vs sensitivity comparisons... depending on the kmer size you get a set of sequences that are unique vs the total amount of unique sequences. If you have too little unique sequences, you can't expand your contigs... if they aren't unique enough you'l ...
written 4.2 years ago by Lesley Sitter540
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Comment: C: explaining N50 to grand mother
... Good point :P but doesn't your index become larger? (there are often more small contigs than large contigs) So if you show it it seems that you have a huge amount of large contigs while in fact your were just looking at it from the wrong side up. ...
written 5.2 years ago by Lesley Sitter540

Latest awards to Lesley Sitter

Scholar 3 months ago, created an answer that has been accepted. For A: How does MAKER decide which proteins go into the final output?
Teacher 3 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 18 months ago, created a question with more than 10,000 views. For A:orthomcl with local mysql server on linux server, complete install
Scholar 18 months ago, created an answer that has been accepted. For A: How does MAKER decide which proteins go into the final output?
Appreciated 3.9 years ago, created a post with more than 5 votes. For A:orthomcl with local mysql server on linux server, complete install
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Removing contigs with improbable coverage using R?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Optimal minimum read length PE HiSeq reads for denovo assembly
Scholar 3.9 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 5.2 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
Teacher 5.3 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 5.4 years ago, created an answer that has been accepted. For A: Maker annotation failure
Scholar 5.4 years ago, created an answer that has been accepted. For A: Maker annotation failure
Autobiographer 5.5 years ago, has more than 80 characters in the information field of the user's profile.
Popular Question 5.8 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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