User: Rory Stark
Rory Stark • 730
- Reputation:
- 730
- Status:
- 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
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... 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 Stark • 730
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... 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 Stark • 730
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... 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 Stark • 730
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... Another Bioconductor package, `DiffBind`, is often used to find differential ATAC peaks using a straightforward ChIP-seq workflow. ...
written 28 days ago by
Rory Stark • 730
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... 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 Stark • 730
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... See reply at https://support.bioconductor.org/p/132502/#132509
...
written 28 days ago by
Rory Stark • 730
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... 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 Stark • 730
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1
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99
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... `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 Stark • 730
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... Default is normalize counts adjusted as follows:
max(chip_counts - control_counts,1)
...
written 8 weeks ago by
Rory Stark • 730
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... 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 Stark • 730
Latest awards to Rory Stark
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4 days ago,
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For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
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4 weeks ago,
created an answer that has been accepted.
For A: [How to Save plots in R] DiffBind
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4 months ago,
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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,
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For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
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14 months ago,
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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For A: How many biological replicates needed for ChIP seq experiments?
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For A: How many biological replicates needed for ChIP seq experiments?
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For A: How many biological replicates needed for ChIP seq experiments?
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For A: Visualization for ChIP-seq analysis
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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For A: How many biological replicates needed for ChIP seq experiments?
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For A: How many biological replicates needed for ChIP seq experiments?
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2.9 years ago,
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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2.9 years ago,
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For A: How many biological replicates needed for ChIP seq experiments?
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
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