User: siklenkak

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siklenkak0
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Posts by siklenkak

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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 1 day 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 ...
tmm deseq2 diffbind chip-seq normalization written 3 days ago by siklenkak0 • updated 1 day ago by Rory Stark1.6k
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Comment: C: Interpretation of cross correlation plot to determine fragment length
... Will do. Thanks a lot!   ...
written 7 days 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 7 days 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 ...
csaw histone chip-seq written 8 days ago by siklenkak0 • updated 7 days ago by Aaron Lun13k

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