User: hwick1

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hwick110
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Posts by hwick1

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Inflating interactionSets into a contact matrix
... I have a list of interactionSets of restriction fragment interactions from a diffHiC experiment, which I extracted using extractPatch. I would like to inflate these into contact matrices, where the row and column names are the restriction fragment coordinates, and the matrix values are the number of ...
diffhic hic interactionset contactmatrix inflate written 23 days ago by hwick110 • updated 23 days ago by Aaron Lun17k
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Comment: C: How to get specific fragment/read interactions from HiC (diffHiC) data?
... One further question, now that I am looking at the results. Am I correct that extractPath only lists the pairs of RE fragments that are interacting? And not the number of times those fragments were found to interact? It seems that entries only occur once, with no "count" of the number of times that ...
written 28 days ago by hwick110
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Comment: C: How to get specific fragment/read interactions from HiC (diffHiC) data?
... Success! Thank you! ...
written 29 days ago by hwick110
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Comment: C: How to get specific fragment/read interactions from HiC (diffHiC) data?
... Thank you, apparently I had some other technical issue that was preventing the update from going through, but I've gotten it to update now. Unfortunately I am getting an error in extractPatch and I can't find what's going wrong: > hs.frag <- cutGenome(BSgenome.Hsapiens.UCSC.hg19, "AAGCTT", ...
written 29 days ago by hwick110
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Comment: C: How to get specific fragment/read interactions from HiC (diffHiC) data?
... Thank you for the speedy response! It seems that extractPatch is a function that is not in the version of diffHiC that I have installed (1.6.0); is github devtools the only method to download the updated diffHiC to get this functionality? ...
written 4 weeks ago by hwick110
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How to get specific fragment/read interactions from HiC (diffHiC) data?
... Hello, I have gone through diffHiC to get significantly interacting bins in my data set. Next, we want to be able to confirm some of these interactions with PCR. To do this properly, I need to be able to see what specific fragments or reads in our significant bins that are doing the actual interact ...
diffhic hic written 4 weeks ago by hwick110 • updated 4 weeks ago by Aaron Lun17k
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Comment: C: min enrichment in peak calling with diffHiC?
... Thank you, I appreciate the advice. ...
written 7 months ago by hwick110
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Comment: C: min enrichment in peak calling with diffHiC?
... I see. Could a  "large number" simply be considered anything greater than the sum of categories 1-5, or is there some other cut-off I should use? Is it better to make the threshold so that >5 category is close to that number? (will I lose anything using that arbitrary 0.5 threshold on my 20kb dat ...
written 7 months ago by hwick110
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Comment: C: min enrichment in peak calling with diffHiC?
... Thank you for the response. The wording there is a bit confusing; I assumed the "less than 5" in "Most of these parents should contain low numbers (i.e., less than 5) of nested bin pairs," referred to the absolute numbers appearing for each category (1,2,3,4,5 and >5). If I understand you correct ...
written 7 months ago by hwick110
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min enrichment in peak calling with diffHiC?
... In 4.4 Peak-calling in the interaction space in the diffHiC users guide, it is suggested to use a "modest" minimum enrichment threshold of 0.5. It is also suggested that most parent bins should have low numbers (<5) of nested bin pairs, and that larger proportions require more aggressive filterin ...
diffhic peak written 7 months ago by hwick110 • updated 7 months ago by Aaron Lun17k

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