Tag: DiffBind

Split merged Bam file without replacement

Split merged Bam file without replacement 0 Hi guys, I have 5 bam (ChIPseq PE data sorted by position) files that came from 5 different murine cortexes (mice that belong to the same group, so biological replicates), however I have a lot of group variability. I’m thinking to merge all…

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Bioconductor – ChIPQC

    This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…

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DiffBind in Bioconda

DiffBind in Bioconda 1 @riba-michela-6472 Last seen 7 weeks ago Italy Hi, I was going to check my scripts for differential ATAC-seq Binding Analysis and wanted to install an updated version of “DiffBind” Bioconductor package, in particular version 3.2.6 or 3.2.4 in whcih a specific little bug that was present…

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Bioconductor – edgeR

DOI: 10.18129/B9.bioc.edgeR     Empirical Analysis of Digital Gene Expression Data in R Bioconductor version: Release (3.5) Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood…

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ChIP-seq analysis differential peak analysis regarding spike-in

ChIP-seq analysis differential peak analysis regarding spike-in 0 Hi, I have 4 human ChIP-seq datasets, including drug A treated H3K4me3 and IgG, and drug B treated H3K4me3 and IgG. Meanwhile, sacCer3 spike-in data is added to human ChIP-seq data. Here is what I did: After aligning, I got 8 bam…

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DiffBind dba.analyze never finishes

I’m running FAIREseq data through the most basic DiffBind pipeline in the tutorial and dba.analyze successfully goes through making final dispersion estimates, then never finishes. I don’t think it’s still running, it’s been over an hour and R is using 0% of my CPU. Did I do something stupid and…

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DiffBind Issue with coordinates

I am analyzing ChIP data. I called peaks with MACS2 run through a RECAP wrapper script. I am attempting differential binding analysis using DiffBind. Code shown below. Please note I have tried the suggestion in biocondutor support from Stark (the developer) to explicitly set the datatype as part of dba.report….

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How does diffbind extract the original coordinates of each difference peak

How does diffbind extract the original coordinates of each difference peak 0 After using dba. analyze() to calculate the difference, use dba. report() to extract the difference peak, but the difference peak coordinates have been merged. How to output the real peak coordinates corresponding to each difference peak in different…

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My ATAC-seq data returns a peak of 1bp for all the peak intervals when using DiffBind’s dba.count(summit=0). why is this happening?

My ATAC-seq data returns a peak of 1bp for all the peak intervals when using DiffBind’s dba.count(summit=0). why is this happening? 0 The binding matrix’s peak intervals (all of them) have a width =1 bp. I have set summit=False, summit=0, summit=True. All these parameters return 1 bp width. In fact,…

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why are all DiffBind tutorial’s ATAC-seq peak intervals 400 bp for all intervals?

why are all DiffBind tutorial’s ATAC-seq peak intervals 400 bp for all intervals? 1 I have followed DiffBind tutorial bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf I have found out that the returned count matrix’s peak intervals are always 400bp. Literally, all the peak intervals in the count matrix are 400 bp. I am wondering why…

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How to import a BED file to ChIPseeker in order to visualize genome coverage plot?

How to import a BED file to ChIPseeker in order to visualize genome coverage plot? 1 Could you please explain how to connect the ATAC-Seq peak results discovered by DiffBind to be imported to ChIPseeker to get CHIP peaks coverage plot? For example, I have the following bed file. chr14…

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How can I export raw count profile from DiffBind to be analyzed on DESeq2 separately?

How can I export raw count profile from DiffBind to be analyzed on DESeq2 separately? 0 I am performing some ATAC-seq analysis. I would like to export the output files as a raw abundance profile so that I can analyze them on DESeq2 separately. I am aware that DiffBind contains…

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DiffBind spike-in normalisation with varying amounts of spike-in chromatin

DiffBind spike-in normalisation with varying amounts of spike-in chromatin 0 Hi there! I am currently using DiffBind v3.2.7 to analyse some ChIP-seq data for RNA Polymerase III (RNAPIII). We have Drosophila spike-in chromatin in the samples that I would like to use in DiffBind to normalise the data. The problem…

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New in DiffBind: dba.plotProfile() – Peak profiles and profile heatmaps

Hi, I am using the new plotProfile function of Diffbind to create some graphs, and get the following error with one subset of my data: dbObj$config$RunParallel <- TRUE profiles <- dba.plotProfile(dbObj) Generating report-based DBA object… Generating profiles… Error in value[3L] : profileplyr error: Error: BiocParallel errors element index: 2 first…

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dba.count reduces binding matrix, why?

dba.count reduces binding matrix, why? 0 db <- dba(samplesheet) This gives me: db 9 Samples, 138044 sites in matrix (193226 total) then I do db.cnt <- dba.count(db) db.cnt 9 Samples, 55893 sites in matrix I wonder why dba.count is removing more than half of the intervals? diffbind atacseq chipseq diffbind3…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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Normalization and differential analysis in ATAC-seq data

Normalization and differential analysis in ATAC-seq data 2 Hello everyone! I would like to know if someone had experiences with normalization and differential expression on ATAC-seq data. After using MACS2 for the peak calling, how can we use Dseq2 or EdgeR on these datas? Someone try this? What is the…

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RPKM on TSS using DiffBind

RPKM on TSS using DiffBind 1 Hi everyone, I want to extrapolate RPKM value from Diffbind. Investigated regions are TSS (± 2.5kb) but around 3500 TSS are “lost” because merged. I have read that in the new version of DiffBind is possible to use dbObj_region$config$mergeOverlap with negative value to avoid…

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low number of significant peaks for one contrast

I am using Diffbind to call differential peaks on an ATAC seq dataset of four conditions (AW, BW, B, and C), and each condition has 2 replicates. One of my replicates (BW2) has low quality (low number of peaks detected by MACS2 compared to the other replicate, and low FRiP)….

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Diffbind adding my own consensus peaks

I’m not entirely sure what you are actually trying to do. Are you trying to add this peakset to use as a consensus peakset for counting? If so you can specify it as a parameter to dba.count() by setting peaks=merged_narrowPeak_sorted without having to load it to look like a sample…

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TMM normalization and sex effect

TMM normalization and sex effect 1 Hello to everyone. I have a doubt about TMM normalization. I’m comparing male versus female samples. Can TMM normalization be affected by the presence of more reads on chromosome x in the female group?? Thanks Francesca edgeR diffbind rnaseq tmm • 75 views It…

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Bioconductor – DESeq2

DOI: 10.18129/B9.bioc.DESeq2     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…

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Bioconductor Forum

James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…

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DiffBind: dba.plotProfile() Change sample order

DiffBind: dba.plotProfile() Change sample order 0 Hi, Is it possible to change the order of samples when using dba.plotProfile()? I’ve tried defining them with the samples= parameter, but I haven’t been successful. I’ve made lovely plots (this is a great tool!), but instead of the default order (ex A, B,…

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