User: j.bergenstrahle

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Posts by j.bergenstrahle

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Comment: C: Rsubread counting peaks ATACseq
... Hi Wei, Thank you for your quick reply. You are indeed correct about the cause of my problem. Sorry for the bad resolution in the picture. The two peaks that you see are overlapping and named differently. allowMultiOverlap=TRUE fixes this, but the real underlying problem in my case is of course the ...
written 23 months ago by j.bergenstrahle80
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Rsubread counting peaks ATACseq
... Hi, I'm about to analyze ATAC-seq data for the first time and my approach atm is: 1. Calling peaks 2. Merge the narrow peaks files into one 3. Convert the merge bed to saf format for input in featureCounts 4. Using featureCounts (Rsubread package) to get counts 5. Use the counts as input to DE ...
rsubread narrowpeaks featurecounts atac-seq written 23 months ago by j.bergenstrahle80 • updated 23 months ago by Wei Shi3.2k
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Answer: A: Diffbind dba.report error
... Hi Rory, I see that I didn't have the latest release. I will use your workaround (works well) until the new release, thanks for the quick reply! Best, JB ...
written 2.5 years ago by j.bergenstrahle80
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Diffbind dba.report error
... Hi! I'm using DiffBind for ATAC-seq data, and everything runs smoothly except one thing -> I cant make a dba.report for one of my contrasts. All steps from loading -> counting -> analyzing seems to work, I get differently called peaks etc. I have 4 different conditions and 6 contrasts (out ...
diffbind written 2.5 years ago by j.bergenstrahle80
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Comment: C: Diffbind data extraction after DE analysis
... Ahh there I go, poorly searched on my side, thanks for the quick answer Gord! ...
written 2.5 years ago by j.bergenstrahle80
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Diffbind data extraction after DE analysis
... Hi, I'm currently using Diffbind for my ATAC-seq pipeline. After calling the dba.analyze function you can do various plots via e.g. dba.plotMA. But is there some simple way to extract the logFoldChange, pvalues etc from the DBA object? I guess this should be easy since the object obviously stores t ...
diffbind written 2.5 years ago by j.bergenstrahle80 • updated 2.5 years ago by Gord Brown590
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Comment: C: fdrtool - correction of p-values - course found on huber.embl.de
... Maybe I should "mark" this question as completed? (Not sure the appropriate approach when posting something like this?)  ...
written 2.6 years ago by j.bergenstrahle80
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fdrtool - correction of p-values - course found on huber.embl.de
... Hello, I originally emailed this question to c Klaus at EMBL and got a really good and well written response. I promised that I should post the question and answer here since more people might find it interesting, especially the approach one might take to explore your data if p-value distributions ...
p-value distribution fdrtool written 2.6 years ago by j.bergenstrahle80

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Popular Question 22 months ago, created a question with more than 1,000 views. For fdrtool - correction of p-values - course found on huber.embl.de
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Student 2.4 years ago, asked a question with at least 3 up-votes. For Rsubread counting peaks ATACseq

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