Tag: DiffBind

What Is The Meaning Of The Score In Diffbind’S Occupancy/Overlap Analysis?

I have 3 chip-seq biological replicates, each with its own input control. I was interested in using diffBind to performs some IDR-style analysis – e.g. take only the peaks that come up in more than one sample. experiment <- dba(sampleSheet=”exp_samples.csv”) pdf(‘overlap_venn.pdf’) dba.plotVenn(experiment, experiment$masks$macs) dev.off() I got a nice Venn diagram:…

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Multi-factor designs in DiffBind

Multi-factor designs in DiffBind 1 Dears, I’m trying to analyze some ChIPseq data using DiffBind. Samples has been processed in two different times SampleID Name Factor IP Condition Replicates 5 PBS_Pol2 S3 Batch1 Pol2 PBS 1 6 PBS_Pol2 S9 Batch2 Pol2 PBS 2 7 C26_Pol2 S4 Batch1 Pol2 C26 1…

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CHIPSEQ Analysis , DiffBind Parameters

CHIPSEQ Analysis , DiffBind Parameters 0 Hello, Regarding Diffbind, How does diffbind calculate common peaks with the samples. I’m observing that certain peaks identified as common using bedtools intersect are not appearing in the output report file generated after DiffBind analysis Command used to write the file : res_deseq <-…

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Cut AND Run , DiffBind Parameters

Forum:CHIPSEQ : Cut AND Run , DiffBind Parameters 0 Hello I have been using DiffBind to perform differential enrichment analysis on my ChIP-seq Cut and Run dataset where I have 2 sample groups, Control and YY1_overexpression, with 4 replicates in each sample group. (Peak Calling was done through SEACR) 8…

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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions

Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions 0 I have an experimental setup where there are known global shifts in levels of our histone mark of interest due to a histone mutation. We include spike-in chromatin in each sample, but we know that the spikein levels are not…

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Diffbind low p-value but high FDR

Diffbind low p-value but high FDR 0 I guess my issue is related to this post support.bioconductor.org/p/85487/#85490. Here is the dba.report(DBA,th=1, bCounts=TRUE) results. One of the peaks clearly shows a significant difference in IGV (And we also expected it to be changed) and has a small p.vaule but the FDR…

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Bioconductor – DESeq2 (development version)

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

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Bioconductor – GenomicRanges

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges. Representation and manipulation of genomic intervals Bioconductor version: 2.14 The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing…

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argument is of length zero

Hi Diffbind community! I have been encountering some errors creating dba object because the Diffbind package can not load the files. I tried using the aligned bam files after creating sample sheet but have been getting following error: “Error in if ((length(callers) == 1) & (callers[1] == “counts”)) { :…

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DiffBind:Using diffbind with only two replicates per condition

DiffBind:Using diffbind with only two replicates per condition 0 I have 6 samples from 3 conditions with two replicates for each condition and I want to make a comparison of these conditions amongst each other. Here is the sample info: SampleID Factor Condtion Replicate PeakCaller 1 Mel239_1 CTCF Mel239 1…

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DiffBind dba.count() crash/can’t finish problems

I am using Diffbind for an ATAC-Seq analysis. My peak caller is MACS2, and here is my sample sheet: I run Diffbind with the following codes, but it crashed every time on dba.count . it can finished Computing summits… Recentering peaks… Reads will be counted as Paired-end. But have this…

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The bam file used for DiffBind?

The bam file used for DiffBind? 1 When use DiffBind to compare ATAC-seq data we need bam file for sample sheet. What kind of bam file do we need? Can I use the bam file which already removed duplicates? OR just primary bamfile? DiffBind ATAC-seq • 351 views You should…

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Spike-in normalization in ATAC-Seq with DiffBind

Spike-in normalization in ATAC-Seq with DiffBind 0 Dear all, we are planning to do an ATAC-Seq experiment in human cell lines and we must correct for batches from different time-points. Therefore, we want to use spike-in normalization as described in the DiffBind vignette. For reasons of practicability, we would prefer…

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ATAC-seq troubleshoot – Just Noise

ATAC-seq troubleshoot – Just Noise 0 Hi everyone, I have been processing paired end 150bp ATAC-seq data, but failing to get peaks at known promoters, the data just looks like noise through out. Started with QC, where reads had poly(G) towards their ends, this is known to happen in NovaSeq…

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Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation

Abstract Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as…

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Genes in open chromatin region

Genes in open chromatin region 0 Hi Biostars friends, I have a questions about bulk ATAc seq that hope you can help. I use Diffbind to get the table below (differential accessibility regions) and then use ChipPeakAnno to annotate the peaks in the P column. Could I conclude that gene…

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Top 25 Bioconductor Interview Questions and Answers

Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. It’s a powerful tool, widely used in bioinformatics and computational biology to process and analyze intricate biological data. Bioconductor’s strength lies in its vast array of packages specifically tailored for genomics research,…

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DiffBind; No sites have activity greater than filter value

DiffBind; No sites have activity greater than filter value 0 Hello I hope you are doing well; I am running into this issue when I am trying to run dba.count(). This is the code I am using: Create a new DBA object using the subset data myDBA <- dba(sampleSheet =…

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Extract RPKM values from Diffbind

Extract RPKM values from Diffbind 2 Hi everyone, does anyone know if there is a way to extrapolate rpkm values from Diffbind?? Thanks Francesca ChIP-Seq Diffbind RPKM • 1.1k views You can set the read score to DBA_SCORE_RPKM in dba.count(). You can do this when you originally count, or anytime…

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Bioconductor – vulcan

DOI: 10.18129/B9.bioc.vulcan     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see vulcan. VirtUaL ChIP-Seq data Analysis using Networks Bioconductor version: 3.15 Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a…

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Assign gene to peak in bulk ATAC-seq

Assign gene to peak in bulk ATAC-seq 0 Hi all, I have some questions about bulk ATAC-seq that I don’t understand, hope that you can help. If we have a task to identify which genes in a sample (such as diseased) are in open chromatin region, is that using differential…

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No contrasts added. There must be at least two sample groups with at least three replicates.

Good morning, I’m working with ATACseq data for the fist time, and I’m using DiffBind for the Differential Accessibility Analysis, but I have this message error when I make the constrast: No contrasts added. There must be at least two sample groups with at least three replicates. I have two…

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Help to get differential_peaks.bed to use for findMotifsGenome.pl?

Help to get differential_peaks.bed to use for findMotifsGenome.pl? 0 Hi all, I am trying to use the command findMotifsGenome.pl from HOMER that needs differential_peaks.bed file as input. I used nf-core/atac-seq then DiffBind but not sure how to get differential_peaks.bed file. Would you please have a suggestion? Do I need to…

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Bioconductor Config

Showing : Config • reset 1 result • Page 1 of 1 Recent … Replies Answer: DEG data by James W. MacDonald 63k This support site is intended to help people who have specific questions about Bioconductor packages, rather than as an advice site meant t… Answer: diffbind by Rory…

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How to compare peak profiles for a subset of ChIPseq genes

How to compare peak profiles for a subset of ChIPseq genes 0 Hello, My goal is to compare the peak profiles between WT and MT strains for a subset of genes in a yeast experiment I have completed. Specifically, I would like to: generate a ranked list of the genes…

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Bioconductor MicroRNAArrayData

Comment: why is downloading the .tar.gz file for a given bioconductor package, then insta by Ndimensional &utrif; 20 Sorry about the N=2. That was meant to read 20 (following the 10 in the previous sentence), my apologies there. The provided link to MSMB-… Answer: smallRNA-seq analysis batch correction in limma…

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Bioconductor – DESeq

    This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see DESeq. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 2.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

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Question regarding lfcShrink types in DiffBind

Question regarding lfcShrink types in DiffBind 0 @aaed3153 Last seen 23 hours ago United States Hello, Rory Stark I have a question regarding the 3 scenarios in which lfcShrink is applied in DiffBind package. The source code looks like this if(shrink) { if(contrast$contrastType==”byname”) { res$de <- suppressMessages(DESeq2::lfcShrink(pv$DESeq2$DEdata, coef=contrast$contrast, lfcThreshold=lfc, res=res$de,type=”apeglm”))…

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atac seq – Help with error DiffBind

Would you please suggest what wrong in this case? I pretty much run the same code as I used for another data set and didn’t have this error. Thank you so much! result <- dba(sampleSheet=samples) result <- dba.blacklist(result) result <- dba.count(result, bParallel=FALSE) result <- dba.count(result) result <- dba.normalize(result) result <-…

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Help with DiffBind Generating report-based DBA object… Error: No valid contrasts/methods specified.

Help with DiffBind Generating report-based DBA object… Error: No valid contrasts/methods specified. 0 Hi all, Would you please suggest what wrong in this case? I pretty much run the same code as before. Thank you so much. result <- dba(sampleSheet=samples) result <- dba.blacklist(result) result <- dba.count(result, bParallel=FALSE) result <- dba.count(result)…

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Missing samples when using function plotProfile() from DiffBind for ATAC-seq

I have 4 samples which are 4 conditions but when I made this plot, I got only 2 conditions. Here is the code I used: samples <- read.csv(“path/to/sample_sheet_DiffBind.csv”) result <- dba(sampleSheet=samples) result <- dba.blacklist(result) result <- dba.count(result, bParallel=FALSE) result <- dba.normalize(result) result <- dba.contrast(result, minMembers=2) result <- dba.analyze(result) dba.plotProfile(profiles) I…

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How to interpret chipseq profile plot

How to interpret chipseq profile plot 1 Hello, I am new to chipseq and generated a profile plot during my diffbind analysis. I was hoping someone could help me understand what the bars straight across mean as profile plots online seem to have various signals around for a site instead…

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How to get genes associated with open chromatin regions?

How to get genes associated with open chromatin regions? 1 Hi all, I ran ATAC-seq pipeline such as nf-core and got output files such as bam, bigwig, broadpeak. Would you suggest a way to get genes associated with open chromatin regions? I used ChIPpeakAnno but for DiffBind. Thank you so…

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Bioconductor Cut&TagData

Answer: error in ChAMP loading file by sophiacruzht • 0 If you ask me what is best outer in cold season then I’m going for the fashionable <a href=”www.hitjacket.com/product/gipsy-danger-… Answer: DESeq2 lfcShrink function used in DiffBind package by ATpoint &starf; 2.9k The DiffBind author will give his own answer, but…

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DESeq2 lfcShrink function used in DiffBind package

DESeq2 lfcShrink function used in DiffBind package 1 @aaed3153 Last seen 9 hours ago United States Hello, We have basically three questions that revolve around the DESeq2 lfcShrink function which is used by DiffBind. We have Cut&Tag samples and want to conduct differential binding analysis. Our main objective is to…

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Profile Plot looks strange

Profile Plot looks strange 0 New to CHiP-Seq. Made a profile plot via diffbind, and it looks very different compared to the ones presented in the vignette. These are just all the samples and sites plotted. Even when I do this for a contrast it still looks odd like this….

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Interpret plots from DiffBind

Interpret plots from DiffBind 0 Hi all, I have 4 samples which are 4 conditions but when I made some plots, I got only 2 conditions.. Does this plot mean ws has chromatin more chromatin open (gain) than wf sample? When I rerun the code, I got all 4 conditions…

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Bioconductor Unevensamplesizes

Answer: multiple filters in biomaRt by RuBBiT0 &utrif; 10 First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro… Comment: Diffbind “No genome detected” by kyliecode • 0 Hi Dr. Stark, Thanks very…

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Which method is the best for using in “dba.count” in Diffbind R package

Normalization in DiffBind has evolved since the original answer a couple of years ago, especially since version 3.0. The default is now to compute the same normalization factors in all the cases your mention. Basically, dba.normalize() is invoked by default in dba.count(), and these values are used for plotting, retrieving…

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CHiP-Seq Questions

CHiP-Seq Questions 0 Hello, New to chip-seq analysis so I apologize in advance for the questions. Currently using diffbind. I see that the interval number for one of the replicates out of the 3 is very high compared to the other 2 replicates. FRiP score across samples is also lower…

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Diff Bind Questions

Diff Bind Questions 0 Hello, Sorry if these questions may seem a bit dumb, I am very new to CHiP-seq and bioinformatics in general. I am trying to use DiffBind to find differential binding between groups. What if a peak is present for a gene in one group but not…

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Help with Diffbind result

Help with Diffbind result 0 @3fdb6f97 Last seen 8 hours ago United States Hi all, I am trying to find which genes are different in chromatin accessibility so I used nf-core/ATAC pipeline then feed the bam files and broadpeak files output into Diffbind. I got around 100k peaks, 21k genes…

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Positive and negative value fold value in ATAC seq using DiffBind

Positive and negative value fold value in ATAC seq using DiffBind 1 Hi all, Does positive fold in this case mean the gene in diseased group is more accessible than the control group? The object is created from the DiffBind package. Thank you so much! I think the answer is…

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Help with error makeTxDbFromGFF in GenomicFeatures package

Hi all, Would you have a suggestion for the error below? Thank you so much. txdb <- makeTxDbFromGFF(opt$gtf) Error in .detect_file_format(file) : Invalid ‘file’. Must be a path to a file, or an URL, or a connection object, or a GFF3File or GTFFile object. opt $cores [1] 1 $help [1]…

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Bioconductor – GenomicRanges (development version)

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…

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Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome

Ethics statement All animal experimentation was conducted according to the National Institutes of Health guidelines for the housing and care of laboratory animals. All experiments were performed in accordance with institutional regulations after review and approval by the Animal Studies Committee at Washington University School of Medicine in St Louis,…

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DiffBind missing peaks and FRiP

DiffBind missing peaks and FRiP 2 I noticed that when I first read in my sample sheet, I get a DBA object with 1226 sites (consensus peaks), yet after running dba.count() on this same object, it is down to 1188 sites. I did not apply any blacklists/greylists. Also, the FRiP…

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Diffbind dba.count doesn’t give FRiP score

Diffbind dba.count doesn’t give FRiP score 1 Hi I am completely new to DiffBind, R and programming in general. I want to use diffbind to analyze peaks called with macs2. When I use dba.count(), I can not get FRiP score at all. I googled this question, but didn’t work. Here…

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how to get raw read counts and normalized read counts

Diffbind: how to get raw read counts and normalized read counts 0 Hi, I want to get raw reads and normalized read count from Diffbind. This is my code: dbObj=dba(sampleSheet = samplesheet) dbObj=dba.count(dbObj, bUseSummarizeOverlaps=T,bRemoveDuplicates = T) datac=dba.normalize(datac,normalize=DBA_NORM_LIB) Then I want to get normalized read count dataframe from this. I try…

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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?

Hello, I am have ChIPseq data from histone marks from 2 different condition (mock and treated with 2 biological replicas each) and the aim of my analysis is to study whether a particular histone mark is enriched in one condition versus the other. I am new to bioinformatic and I…

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DiffBind reports no significant differentially enriched peaks

Hello I have been using DiffBind to perform differential enrichment analysis on my ChIP-seq dataset where I have 2 sample groups, WT and KO, with 4 replicates in each sample group. The analysis reports only 2 significantly differential enriched peaks at FDR < 0.05, and the situation does not change…

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How to quantify the reads of each peak for ChIP-seq data?

How to quantify the reads of each peak for ChIP-seq data? 1 Hello I can quantify the total reads of all the peaks in a peak file using DiffBind, the tamoxifen.csv: SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller BT4741 BT474 ER Resistant Full-Media 1 reads/Chr18_BT474_ER_1.bam BT474c…

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Chip-seq Analysis

Chip-seq Analysis 0 Hi everyone, I am analyzing chipseq data and I am trying to figure out the handling of biological replicates and the best tools to use. I tried to dig into the former questions, but it is hard to navigate thorough so many information. I have 2 different…

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FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer

Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249 (2021). Article  PubMed  Google Scholar  Sanli, O. et al. Bladder cancer. Nat. Rev. Dis. Prim. 3, 17022 (2017). Article  PubMed  Google Scholar  International…

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DiffBind analysis report gives me two different outputs depending on when I apply a filtering threshold [eg: P-value=0.05, (abs)FC=1.1]

DiffBind analysis report gives me two different outputs depending on when I apply a filtering threshold [eg: P-value=0.05, (abs)FC=1.1] 1 Why is there a difference between the report outputs I get after dba.report, with a threshold set to P-value = 0.05 and fold=0.13750352375 [to get (abs)logFC=1.1], compared to when I…

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Bioconductor – DiffBind

DOI: 10.18129/B9.bioc.DiffBind     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DiffBind. Differential Binding Analysis of ChIP-Seq Peak Data Bioconductor version: 3.15 Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions….

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Strange results from Diffbind-Deseq2 differential peak binding of cfChip-seq with blocking

Strange results from Diffbind-Deseq2 differential peak binding of cfChip-seq with blocking 1 Hi All, I am working on cfChip-seq with the goal of comparing differentially bound peaks between two timepoints. Please note that same patients (n = 9) donated samples on the two occasions. Our quick PCA analysis showed a…

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Quantifying Peak Height Difference in ATAC-seq

Quantifying Peak Height Difference in ATAC-seq 1 Hi, everyone. How would I go about quantifying the peak height difference of a particular gene between two a wild type and a mutant in ATAC-seq? A colleague mentioned possibly calculating a moving average of read depths for smoothing and then comparing the…

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DESeq2 analysis has not been run for this contrast

DESeq2 analysis has not been run for this contrast 1 @e16bdcce Last seen 10 hours ago Hong Kong error :DESeq2 analysis has not been run for this contrast DB.DESeq2 = 0 I think until this step everything is ok here is my file↓ here is my code ↓ # dbObj_contrast…

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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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