Tag: DiffBind

Answer: multiple filters in biomaRt by RuBBiT0 ▴ 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…

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…

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…

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…

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…

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…

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]…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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….

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…

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…

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…

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…

    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…

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…

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…

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…

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…

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….

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…

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,…

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…

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…

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…

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…

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…

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…

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)…

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…

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…

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)….

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…

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…

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…

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…

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,…