User: Rory Stark

gravatar for Rory Stark
Rory Stark490
Reputation:
490
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Trusted
Location:
University of Cambridge, Cancer Research UK - Cambridge Institute
Last seen:
3 months, 1 week ago
Joined:
4 years, 7 months ago
Email:
r*********@cruk.cam.ac.uk

Posts by Rory Stark

<prev • 21 results • page 1 of 3 • next >
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Answer: A: create a RC matrix with narrowPeak data
... The DiffBind package in Bioconductor creates a read count matrix from peak calls and aligned reads. ...
written 3 months ago by Rory Stark490
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Answer: A: How to correlate chip seq peaks?
... I'm not sure how two peaks could be considered "similar" if their locations are several kb apart? We usually think of peaks being the same in replicates if their coordinates at least overlap. That said, a very easy way to get pearson or spearman correlation values is to read all the peaksets into t ...
written 4 months ago by Rory Stark490
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Comment: C: question about DiffBind
... This is telling `DiffBind` to look in a specific directory within the package installation for the samplesheet file. This is very non-standard -- it only looks there for the example samplesheet as this is part of the installation itself. The specific error is that the first peak file doe not exist w ...
written 4 months ago by Rory Stark490
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Answer: A: Diffbind for ATAC-seq data with no controls
... Control reads, such as those from an Input sample, are optional in DiffBind, so you can just leave out the control column in the sample sheet. ...
written 5 months ago by Rory Stark490
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Answer: A: Diffbind - Very high proportion of significant peaks
... I have certainly see this level of differentially Some questions: - Do you expect the conditions to change the open chromatin landscape quite a bit? - How are the differential sites divided between the two conditions? Do they mostly show increases in one condition, or are there many ch ...
written 7 months ago by Rory Stark490
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Answer: A: Diffbind error : sequences from an unspecified genome; no seqlengths
... Has this been resolved? You shouldn't need to specify the genome as DiffBind takes the chromosome names directly from the peak files, so if they are consistent it should work. However there was a bug at some point that impacted this in certain cases. What version of DiffBind are you using? Alterna ...
written 7 months ago by Rory Stark490
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Answer: A: What is the best method ChIPseq differential binding analysis?
... Disclosure: I am the author of `DiffBind`, a differential binding analysis tool. Interestingly, the tools you are considering are not the ones most often used to derive results in the published literature. `MACS` + `DiffBind` is by far the most widely used combo for experiments with multiple biolog ...
written 9 months ago by Rory Stark490
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Comment: C: DiffBind - Erroneous Affinity Shift In One Direction
... Can you confirm which version you are using from `sessionInfo()`? I'm limited in what I can do without examining the object, but here's a few things to look at. Something is going on in counting the A sample peaks. Look at them un-normalized (`bNormalized=FALSE`). If they are all 1 then nothing is ...
written 9 months ago by Rory Stark490
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Answer: A: DiffBind - Erroneous Affinity Shift In One Direction
... Hello, I am the author of `DiffBind`. 1) There are a number of things that could account for the A-B differences. You say all the shifts are in one direction, which I assume means that the fold-changes of all the differentially bound (DB) sites have the same sign? It may be instructive to look at t ...
written 9 months ago by Rory Stark490
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Answer: A: Diffbind package DESeq2 analysis
... The most obvious answer would be that there may not be any significantly deferentially bound peaks in your experiment. This could be due to the biology (nothing is changing) or be related to the experimental design. For example, the experiment could be underpowered, mostly likely due to not having e ...
written 10 months ago by Rory Stark490

Latest awards to Rory Stark

Scholar 5 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 9 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 13 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 13 months ago, created an answer that has been accepted. For A: Visualization for ChIP-seq analysis
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 13 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 13 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Popular Question 4.1 years ago, created a question with more than 1,000 views. For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
Appreciated 4.5 years ago, created a post with more than 5 votes. For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments

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