User: Anton Goloborodko

Reputation:
250
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Trusted
Location:
USA/Cambridge/MIT
Website:
http://mirnylab.mit.edu/
Twitter:
golobor
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Last seen:
2 years, 8 months ago
Joined:
9 years, 7 months ago
Email:
g****************@gmail.com

Posts by Anton Goloborodko

<prev • 12 results • page 1 of 2 • next >
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Comment: C: What is meaning of true diagonal in Hi-C?
... uuuggghh, not really! :) The [4DN consortium][1] is currently working on Hi-C data analyses standards, which will address this issue, among others. Though, it will take some time to produce a document. Meanwhile, I'd recommend my all-time favorite [guideline to Hi-C data analysis][2] by Noam Kaplan ...
written 3.6 years ago by Anton Goloborodko250 • updated 3.6 years ago by PoGibas4.8k
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Answer: A: What is meaning of true diagonal in Hi-C?
... The true diagonal contains contacts between loci separated by distances below the size of a bin. The 2nd diagonal has such contacts too, i.e. contacts between pairs of loci located close to the bin boundary, but on the either side of it. Our lab's usual recommendation is to discard two first diagon ...
written 3.6 years ago by Anton Goloborodko250
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Answer: A: How to generate contact probability graph from mapped reads?
... Hi! Sounds like you are trying to assemble a map of 3d interactions from a sequenced Hi-C library? There is quite a few pieces of software that can help you out with this task: http://data.genomegitar.org/4DN_software.php. [Our lab][1] is developing a python library [hiclib][2], which I could recomm ...
written 4.0 years ago by Anton Goloborodko250
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Answer: A: Read depth and Hi-C resolution
... Hi, the resolution of a Hi-C dataset (a) highly depends on the details of the protocol and (b) actually, is a poorly defined, though real measure. (a) the number of reads is not the only variable that determines the quality of a Hi-C dataset. First, if the total number of unique Hi-C molecules i ...
written 4.0 years ago by Anton Goloborodko250
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Answer: A: How to list genomic regions that are close in a 3D conformation manner using Hi-
... Hi, it sounds that the normalized Hi-C contact frequency between two loci of interest would indeed be the measure that you are looking for. Though, there are at least two caveats. (A) The 3d conformation of a genome varies greatly from nucleus to nucleus, so that two regions that are close to each ...
written 4.0 years ago by Anton Goloborodko250
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Comment: C: Chromosomal breakpoints and Hi-C data
... Hi! I'm not entirely sure, which paper you mean by this? ...
written 4.0 years ago by Anton Goloborodko250
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Answer: A: Looking For Information On Hi-C (Chromosome Conformation Capture) Analysis: Work
... I would recommend [a recent review of Hi-C data analysis][1] by Job's Dekker lab. It gives a nice overview of the features of Hi-C data and the method itself, which is arguably more important right now than particular mathematical models of these features. [1]: http://www.ncbi.nlm.nih.gov/pubmed/ ...
written 4.1 years ago by Anton Goloborodko250
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Answer: A: Chromosomal breakpoints and Hi-C data
... I don't think there is any published method to find breakpoint regions with Hi-C (personally, I doubt it is even possible). You can, however, detect possible chromosomal rearrangements in your sample, at least for mammalian cells. The method is based on the fact that, in mammalian cells, we still ...
written 4.1 years ago by Anton Goloborodko250
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Comment: C: Does The Urushiol (Poison Ivy) Mutation Predate Humanity?
... Also, notice that poison ivy and poison oak doesn't grow outside North America, which was populated late after Homo Sapiens was formed. ...
written 8.6 years ago by Anton Goloborodko250
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Answer: A: How Do You Maintain Flexibility In Your Code, When You Don'T Know In Advance Whi
... My experience is based mostly on solo projects and is in accordance with the other answers. I like to start with a simplest project layout and then elaborate and refactor it if needed. There are a few points/techniques I want to emphasize: Usually my standard projects start with two directories, ./ ...
written 8.6 years ago by Anton Goloborodko250

Latest awards to Anton Goloborodko

Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Chromosomal breakpoints and Hi-C data
Scholar 4.1 years ago, created an answer that has been accepted. For A: Chromosomal breakpoints and Hi-C data
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Chromosomal breakpoints and Hi-C data
Good Question 8.9 years ago, asked a question that was upvoted at least 5 times. For Which Mass-Spectrometry Search Algorithm Do You Use For Peptide/Protein Identification?
Student 8.9 years ago, asked a question with at least 3 up-votes. For Which Mass-Spectrometry Search Algorithm Do You Use For Peptide/Protein Identification?

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