User: Rory Stark

gravatar for Rory Stark
Rory Stark730
Reputation:
730
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Trusted
Location:
University of Cambridge, Cancer Research UK - Cambridge Institute
Last seen:
1 day, 2 hours ago
Joined:
6 years, 3 months ago
Email:
r*********@cruk.cam.ac.uk

Posts by Rory Stark

<prev • 43 results • page 1 of 5 • next >
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Answer: A: diffBind dba.count error for a peaks file selected
... The issue could be related to running this in the default parallel mode. How many samples do you have? By default `dba.count()` will grab all the cores on your machine and attempt to count each sample in parallel. If you have a lot of "peaks" (all CpGs!), this could take a lot of memory for each par ...
written 24 days ago by Rory Stark730
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Answer: A: Extract RPKM values from Diffbind
... RPKM values are much lower in general than read counts. The first step is to divide by how many million sequence reads you have in your library. So if you sequenced to a depth of 20M reads, all the counts would be divided by at least 20. Here's how it's implemented in `DiffBind`: rpkm <- ...
written 28 days ago by Rory Stark730
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Comment: C: DiffBind gives peaks of different widths, even when setting "summits"
... Note that if you run dba.count() again using the consensus peaks from the first call, it will find the summit of the merged peak and re-center, leaving you with all peaks the same width (but one fewer peak).. ...
written 28 days ago by Rory Stark730
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Answer: A: are there some tools or software can find the different peak of ATAC-seq
... Another Bioconductor package, `DiffBind`, is often used to find differential ATAC peaks using a straightforward ChIP-seq workflow. ...
written 28 days ago by Rory Stark730
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Answer: A: Extract RPKM values from Diffbind
... You can set the read score to `DBA_SCORE_RPKM` in `dba.count()`. You can do this when you originally count, or anytime after by calling DBA <- dba.count(DBA,peaks=NULL,score=DBA_SCORE_RPKM) Then you can retrievethe RPKM values in a `GRanges` object (or `data.frame`): rpkm <- dba.pe ...
written 28 days ago by Rory Stark730
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Answer: A: why DiffBind, diffferentially binding site is the for different samples
... See reply at https://support.bioconductor.org/p/132502/#132509 ...
written 28 days ago by Rory Stark730
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Answer: A: How to make complex contrasts in DiffBind dba.contrast
... In the current version, `DiffBind` does not support complex model designs and contrasts. However in the next release (currently in the development version), arbitrary model designs and complex contrasts are supported. Ir order to get the contrast you want, you'll need to reconfigure your metadata a ...
written 29 days ago by Rory Stark730
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Answer: A: DiffBind gives peaks of different widths, even when setting "summits"
... `DiffBind` always merges overlapping peak intervals. In your case, when you center around summits to get 1001pp intervals (500bp up and downstream of the summit), some of those 1k intervals themselves overlap and are merged. ...
written 4 weeks ago by Rory Stark730
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Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
... Default is normalize counts adjusted as follows: max(chip_counts - control_counts,1) ...
written 8 weeks ago by Rory Stark730
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Answer: A: DiffBind error when calling dba.count
... Is there a subdirectory named `data` in your current working directory with the bam files? Try: > file.exists("data/alignment_output/10A_1_H3K_aligned.bam") There also need to be a matching index file (.bai) for each bam. ...
written 9 weeks ago by Rory Stark730

Latest awards to Rory Stark

Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Scholar 4 weeks ago, created an answer that has been accepted. For A: [How to Save plots in R] DiffBind
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Scholar 2.2 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.2 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
Teacher 2.3 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
Scholar 2.5 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.5 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
Scholar 2.8 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Visualization for ChIP-seq analysis
Teacher 2.8 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
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 2.9 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.9 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
Scholar 2.9 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.9 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
Teacher 4.9 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 5.8 years ago, created a question with more than 1,000 views. For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments

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