User: Ian Donaldson

gravatar for Ian Donaldson
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Posts by Ian Donaldson

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DESeq - ChIP-seq (including background reads)
... I have previously used DESeq to analyse differential binding in ChIP- seq data (2 replicates of two ChIP samples). I believe the newer versions of DESeq (i have 1.6.1) are able to consider the matching input samples to correct for the background reads. Does anyone have experience of including the ...
deseq written 7.4 years ago by Ian Donaldson70 • updated 7.4 years ago by Gordon Brown70
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htSeqTools - filtered reads > BED?
... I have found the htSeqTools methods useful for creating PCA plots of samples. The filtering of reads to remove those that are deemed to be over amplified looks very interesting. The function is called like this: # BAM to IRanges object: reads01 <- readAligned(dirPath , "reads01.bam", type='BAM' ...
iranges htseqtools written 7.4 years ago by Ian Donaldson70 • updated 7.4 years ago by Michael Lawrence11k
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htSeqTools - naming RangedData objects?
... I am trying to get htSeqTools to create a PCA for my ChIP-seq sample reads. However, by default there are no labels associated with the sample points in my PCA plot. METHOD: I created RangedData objects like this, e.g: RR05 <- readAligned(dirPath , "RR_20111013_filtered_RR05_bfast_hg18_a3 _best ...
htseqtools assign written 7.4 years ago by Ian Donaldson70 • updated 7.4 years ago by Michael Lawrence11k
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Comment: C: Using DESeq with ChIP-seq data - all or non-redundant reads?
... Thank you for your response Ivan! I completely agree that removing duplicates is a necessary step for peak calling. I seems as though keeping duplicates is a "double edged sword" where it is not easy to separate PCR artifactual reads from real ones. I think what, to me, makes using all the reads ...
written 7.7 years ago by Ian Donaldson70
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Using DESeq with ChIP-seq data - all or non-redundant reads?
... I have been using DESeq to look at differential binding in ChIP-seq for a while now. But recently we have been discussing locally whether the ChIP-seq reads used in DESeq should be the full or non-redundant set? There is a worry that the full set of reads may contain spuriously amplified reads, bu ...
deseq written 7.7 years ago by Ian Donaldson70 • updated 7.7 years ago by Ivan Gregoretti310
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Comment: C: Using DESeq with ChIP-seq data
... Thank you for your reply Simon. Just to clarify I run MACS on duplicates of the same TF at two time points: 2x TF at time point A vs control 2x TF at time point B vs control Sorry for being slow, but i dont see how pooling all the reads will allow me to distinguish between the two time points? Ia ...
written 7.9 years ago by Ian Donaldson70
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Using DESeq with ChIP-seq data
... I am new to DESeq, so apologies if this is a simple question! I am planning to use DESeq to compare ChIP-seq sample binding regions, but i am wondering what the best method of running DESeq might be. I have several thoughts about this, what would you suggest? The initial problem i see is that the ...
deseq written 7.9 years ago by Ian Donaldson70 • updated 7.9 years ago by Simon Anders3.5k

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