User: tlgolan

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Posts by tlgolan

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r3Cseq and rat genome
... I am about to analyze my 4Cseq data, and thought of using r3Cseq package. My reads are aligned to Rn6 genome. Does the package fits to this kind of genome? If not, does it solvable? Thanks! ...
r3cseq 4cseq written 3.0 years ago by tlgolan0
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4C-ker and Rat genome
... Hi, Does anybody know if I can use the package 4C-ker for Rn6 genome? Thanks ...
4c-ker written 3.1 years ago by tlgolan0 • updated 3.1 years ago by James W. MacDonald50k
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FourCseq- adding information manually
... Hi, I am trying to manually add information (rowRanges and primer data) to my 'fc' object. This is my code (the relevant parts to my problem): fragmented_Rn6=read.table(file="valid fragments only_Rn6.tab",header=TRUE)  fragmented_Rn6$leftSize=as.numeric(fragmented_Rn6$leftSize) fragmented_Rn6$righ ...
fourcseq written 3.1 years ago by tlgolan0 • updated 3.1 years ago by felix.klein150
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Comment: C: local fit and FourCseq
... Hi Felix, When I chose minCount=372, I got a parametric fit. The problem is that this threshold left me with ~480 fragments only. I believe that this is a very low number of fragments. Is it enough to go on with the analysis? Thanks again, Tal  ...
written 3.1 years ago by tlgolan0
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Comment: C: local fit and FourCseq
... Hi Felix, Thanks for your quick answer. I tried to use parametric fit, but a local fit was automatically substituted it. How can I 'force' parametric fit to my data? Thanks, Tal  ...
written 3.1 years ago by tlgolan0
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FourCseq and local fit
... Hi, I am trying to analyze my 4Cseq data using the FourCseq package.  I have some difficulties while running the getZscores function; I keep getting this Error:  gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well capt ...
fourcseq written 3.1 years ago by tlgolan0
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local fit and FourCseq
... Hi, Did anyone succeed to run the function getZscore while using local fit?  If so, please share.   ...
fourcseq local fit written 3.1 years ago by tlgolan0 • updated 3.1 years ago by felix.klein150
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How to remove aberrant chromosomes from a BSgenome object?
... Hi everyone, How can I remove mitochondrial chromosome and aberrant chromosomes ("_" pattern) from a BSgenome object? I am trying to create such object that contains only chr1-20 and X,Y chromosomes (Rn6 genome). Thanks! ...
bsgenome R written 3.2 years ago by tlgolan0 • updated 3.2 years ago by Hervé Pagès ♦♦ 14k
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FourCSeq- without replicates
... Hi, Does anyone know if I can use FourCSeq on my 4Cseq data in case that my data doesn't contain replicate samples? Thanks, Tal ...
fourcseq written 3.2 years ago by tlgolan0 • updated 3.2 years ago by felix.klein150
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Comment: C: error while running Basic4CSeq
... Hi Shruti, Did you solved this problem? I am having the same one while using Basic4Cseq on my 4Cseq data. Thanks, Tal ...
written 3.2 years ago by tlgolan0

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