User: jotan

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jotan1.2k
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Posts by jotan

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Comment: C: Low input ChIP-seq on frozen tissue
... "Why would you think the antibodies cannot bind to the proteins?" I was mostly thinking protein degradation. I suppose the only way to find out is to try. Good luck! ...
written 5 months ago by jotan1.2k
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Comment: C: Low input ChIP-seq on frozen tissue
... I would be most concerned about the protein quality. Most ChIP protocols have fixation as the first step to preserve protein structure and DNA interactions. Would antibodies continue to bind proteins from a thawed sample? ...
written 5 months ago by jotan1.2k
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Comment: C: Trying to get exact chromosome 17 position for a promotor region of the serotoni
... It's not really clear what you're trying to do. What WGS data are you working with? How long are the reads? Are you looking for a long insertion/deletion in the WGS dataset(s)? If that's the case, then it seems as if you might have to do a de novo assembly rather than mapping onto a reference. ...
written 5 months ago by jotan1.2k
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Comment: C: Does allele refer to the entire gene sequence or one position of the gene sequen
... I don't want to argue, and I don't even necessarily disagree with you but: "The fact is, you can argue until you're blue in the face about how a definition should be used in a certain way, and about how all the people using it in another way are wrong, but if the majority are using it that way then ...
written 15 months ago by jotan1.2k
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Comment: C: Does allele refer to the entire gene sequence or one position of the gene sequen
... I was a little too hasty in my reply. On closer reflection, I don't actually define an allele as a whole gene. I think my definition is more like "sequence variants in a population within a given window (>1bp) of DNA sequence". I personally think it's silly to refer to a single base pair as an ...
written 15 months ago by jotan1.2k
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Answer: A: Does allele refer to the entire gene sequence or one position of the gene sequen
... "1) Does allele refer to the entire gene sequence or one position of the gene sequence?" The short answer is: An allele is a complete gene sequence. "Here we refer to allele as one base of a gene." That is an incorrect (or highly contentious) definition of an allele. One base change in a gene is ...
written 15 months ago by jotan1.2k
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Answer: A: prediction form DNA (A,B,Z) by sequence
... This database predicts non-B DNA structures [Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.][1] But be careful. Lars Juhl Jensen is absolutely right, you need to be very careful in interpreting a *prediction* [1]: https://nonb-abcc.ncifcrf.gov/apps/si ...
written 16 months ago by jotan1.2k
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Answer: A: Heteroplasmy and homoplasmy in mtDNA
... Homo = Same (1 type) Hetero = Different (>1 type) A mammalian cell has a single nucleus which contains a single genome. The genomic DNA is identical across all cells in an organism. A mammalian cell has many mitochondria and every mitochondria has its own (circular) genome. All the many indivi ...
written 16 months ago by jotan1.2k
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Comment: C: EMBL-ABR: standards in biosciences
... Some of the questions in the survey are quite ambiguous. Particularly Q3. "Which standards do you use for your data and for which purpose?" I'm not sure I understand what is meant by "standard" in this context. Does it refer to: 1) A benchmark? (e.g. gold standard) 2) A control? (e.g. normalisati ...
written 16 months ago by jotan1.2k
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Comment: C: CpG islands density calculation
... Two quick notes: You should probably normalise for lengths. Are these sequences directional? Should you include an inverse pattern of "GC", given DNA is double stranded. ...
written 16 months ago by jotan1.2k

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Popular Question 6 months ago, created a question with more than 1,000 views. For Identifying novel ChIP-seq peaks in KO samples compared to WT
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Do bioinformaticians often break molecular biologists' hearts by being the first
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Scholar 2.2 years ago, created an answer that has been accepted. For A: Gene to coordinates
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Scholar 2.7 years ago, created an answer that has been accepted. For A: Gene to coordinates

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