User: siklenkak

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siklenkak0
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Posts by siklenkak

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Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
... Hi, I was reading this question and found I have a similar problem to the op, Igor. I'm also trying to figure out the effects of normalization on my data.  Initially, I suspect that we would have a global change in our treatment vs control so based on the logic described throughout the literature bF ...
edger diffbind deseq2 chip-seq written 2.2 years ago by siklenkak0 • updated 2.2 years ago by Rory Stark2.8k
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Comment: C: Clarification on Normalization Approach in DiffBind's db.analyze()
... Hi Rory,  Thanks for the quick response; however, I will follow up with a question about that. The Anders and Huber 2010 DEseq paper describes the median ratio method, also implemented in DESeq2.  As you know, this function is described as DEseq2::estimateSizeFactors(), but from what I can tell ta ...
written 2.3 years ago by siklenkak0
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Clarification on Normalization Approach in DiffBind's db.analyze()
... Hi to all, Simple question for DiffBind that isn't clear to me despite a lot of searching and (over) thinking. How exactly is the count data treated when one invokes db.analyze(method=DESeq2) using default parameters in current release?  My understanding is that some years ago the devs set bFullL ...
normalization diffbind deseq2 chip-seq tmm written 2.3 years ago by siklenkak0 • updated 2.3 years ago by Rory Stark2.8k
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Comment: C: Interpretation of cross correlation plot to determine fragment length
... Will do. Thanks a lot!   ...
written 2.3 years ago by siklenkak0
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Comment: C: Interpretation of cross correlation plot to determine fragment length
... Hi Aaron, thanks for your answer.  Sorry to not mention that this is H3K4me3 data from mouse sperm cells which are a-typical and have only ~1% of the nucleosomes present in somatic cells. These nucleosomes are mainly retained at TSS and preferentially enrich at CpG dense regions.  Median peak width ...
written 2.3 years ago by siklenkak0
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Interpretation of cross correlation plot to determine fragment length
... Hi, I have a question about interpreting my cross-correlation plots from native ChIP-seq data with 100bp SE reads aligned uniquely to the genome using bowtie2.  The bam files have duplicates marked and removed for this step. To estimate fragment length I used  correlateReads() from the csaw packag ...
chip-seq csaw histone written 2.3 years ago by siklenkak0 • updated 2.3 years ago by Aaron Lun23k

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