Bioconductor Forum

Hello everyone! I've run the nf-core Cut&Run pipeline on five samples, each with three replicates, using IgG as a control and an E. coli spike-in for normalization. The pipeline normalization was set to spike-in...Hello everyone! I've run the nf-core Cut&Run pipeline on five samples, each with three replicates, using IgG as a control and an E. coli spike-in for normalization…

Normalization DiffBind

updated 14 months ago • kim

which mentions that "More complex schemes, such as forming a consensus peak set separately from the replicates for each condition and then taking the union of these, are also possible." Is there guidance somewhere to do this...How can this be done with Diffbind? Thank you, Ian

DiffBind

updated 21 months ago • Ian D.

Hi, I am performing DiffBind on ATACseq data and I have a question regarding the use of block and design in setting a dba.contrast. From a previous...be different now in the new version as the design setting has changed. I would like to block for replicate (or individual patient in my case) whilst also using a design that includes Tissue as confounder: ~Tissue + Condition...However, when I do t…

DiffBind R ATACSeq

updated 4.5 years ago • fleur_p90

data similar to ChIP-Seq) after degradation of my protein of interest. I am currently using Diffbind in combination with DESeq2 method of dba.analzye() but diffbind provides so many different options for dba.normalize...when using Option 1 vs Option 2 in dba.normalize(). Thank you! ```r #Importing the the table for diffbind containing all the necessary files, names, and locations CTCF_narrowp…

GenomicLocalization DESeq2 Cut&Run Diffbind Normalization

updated 5.1 years ago • Monica

Hi I am using diffbind package to analyze my Chip seq data. I have bed files in my hand. I have arranged my input sample sheet (PFA). I am getting...this error. Could you please help me to solve this issue? > library(DiffBind) > Data <- dba(sampleSheet="SampleInfonew.txt") 1 NA raw Error in if (is.na(peaks)) { : argument is of length zero Reg…

DiffBind ChIPchip

updated 5.0 years ago • shrinka.genetics

<div class="preformatted">Hi Walter - You did the right thing by explicitly calling dba.contrast to add the WT vs KO contrast as there are only two knockouts. However you have two different factors (trimethyl and monomethly, I assume these are histone marks) for each condition. The warning from dba.analyze is that there were no differentially bound sites identified (with an FDR < …

Cancer edgeR DiffBind Cancer edgeR DiffBind

updated 13.0 years ago • Rory Stark

samples divided into 5 conditions, such as A, B, C, D, E. All samples are from different tissues, no replicate. I want to differentiate them according to 5 conditions by DiffBind package, and display result on heatmap. So I did

diffbind

updated 7.5 years ago • mengm5

<div class="preformatted">Dear list, --I'm trying to use Diffbind package to analyze some samples from a ChIP seq experiment. --I created a .csv samplesheet with the following fields and which samples to analyze: SampleID Tissue Factor Condition Replicate Reads Control Peaks Chip_K27.1+ Neural K27 Responsive 1 Chip_K27.BED Input_K.BED Chip_K27.BED Chip_K27.2+ Neural K27 Responsiv…

DiffBind DiffBind

updated 13.1 years ago • José Luis Lavín

are deferentially bound between two sample groups. I've read through the [Bioconductor manual for Diffbind](http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf), but I do not understand...knowledgeable in programming languages. I'm wondering how much I need to learn to be able to perform Diffbind on my ChIP-seq datasets. Are there any Diffbind tutorials/guides …

diffbind chip-seq

updated 8.5 years ago • AA

Happy new year folks !!! I used the Diffbind vignette and ran the commands provided in Rstudio. However, the Intervals in the dba object do not match with the...vignette. It would be great if you could help me out with this. Thanks in advance. ``` dba object in Diffbind vignette > tamoxifen 11 Samples, 2845 sites in matrix (3795 total): ID Tissue Factor Condition Treatment Replicate...…

DiffBind

updated 4.0 years ago • Ayyappa

11 Samples, 2845 sites in matrix (3795 total): ID Tissue Factor Condition Treatment Replicate Intervals 1 BT4741 BT474 ER Resistant Full-Media 1 2 2 BT4742 BT474 ER Resistant Full-Media 2 3 3 MCF71 MCF7 ER Responsive...Full-Media 2 7 ''' This is what the Rstudio console displays > library(DiffBind) L…

DiffBind

updated 4.0 years ago • Ayyappa

and the other that is lacking the FLAG tag. Samples were taken at 2 timepoints, from 2 biological replicates and I also have a total DNA control.</span> <span style="line-height:1.6">I first used MACS2 to normalize every ChIP sample...200bp-2kb and this corroborates what I see when I view the BAM files in IGV.</span> I then used DiffBind to look for peaks that are significantl…

diffbind

updated 10.7 years ago • dsherw

Hello, Thanks for your effort in producing such a good tool for analysis. Recently, I am using Diffbind to characterize differential open chromosome regions with ATAC-seq. I have more than 50 samples, equipping with...Hello, Thanks for your effort in producing such a good tool for analysis. Recently, I am using Diffbind to characterize differential open chromosome regions with ATAC-seq. …

DiffBind

updated 3.3 years ago • littlefishes20

Hi I am using Diffbind to report the DBS (I know that SICER has already a tool for doing so, but I have a huge dataset with different treatments...and I just want to try with DiffBind) In any case, have you ever tried it? Even if the results that I get are good and consistent with other peak callers, it

Sicer diffbind

updated 10.8 years ago • sergio.espeso-gil

wherein I am given a few BED and BAM files to analyse and see how similar they are. I am using the diffbind package to do so. The first correlation map(heat map), when I run >>>MB <- dba(sampleSheet="MBdataframe.csv")&nbsp...very simple manner using 3 BED and corresponding BAM files and not complicating it by Conditions and replicates etc for now(I don't have that…

diffbind heatmap

updated 9.6 years ago • shubhibartaria

Hi,  I can run DiffBind well before. However, after I updated R 3.2.0, R RStudio 0.99.441, and DiffBind 1.14.4, the DiffBind cannot be used anymore...nbsp;   there is no package called ‘GO.db’ Error: package or namespace load failed for ‘DiffBind’ I have install GO.db & DiffBind many times, but it doesn't work. Could you give me a help? Many thanks. Gary <img al…

diffbind go.db

updated 10.6 years ago • Gary

Hi,  I am using DiffBind to assess the H3K27me3 chipseq binding differences between two conditions. I am using default settings. I would...Hi,  I am using DiffBind to assess the H3K27me3 chipseq binding differences between two conditions. I am using default settings. I would like to visualize differentially bound regions in IGV/UCSC Genome Browser. I have generated RPM normali…

Rory Stark diffbind TMM edgeR chipseq

updated 9.6 years ago • akdess

Hi, I'm having issue with dba.contrast() in DiffBind v3.4.0. I have two conditions, and each condition has 3 replicates. I'm working a simple differential peak analysis

v3.4.0 DiffBind

updated 4.2 years ago • AMA

Hi everyone! When we prepare the sampleSheet matrix for the DiffBind::dba function, we may have 2 columns for bam files - 1 for ChIP bam and 1 for Input/IgG bam. Here I have 2 bam files for ChIP...bams into two different rows on the same column? My 2 bam files for ChIP(IgG) are actually from 2 replicates. My purpose of doing things above is to merge replicates - which of course can be done in…

DiffBind chipseq

updated 2.3 years ago • lin.pei26

div class="preformatted">Dear All, I am using package DiffBind, Due to the fact that I miss real biological or technical replicates, I am assesing the overlapping rates between...different peak callers. Here is how I set up my database to read in: 3 Cell lines, 4 Factor, 2 Replicates, for a total of 12 Conditions > rm(list=ls()) > setwd("/home/pkunderf/output/DiffBind/ES-CMN-CM…

CMA DiffBind CMA DiffBind

updated 13.5 years ago • Paolo Kunderfranco

Normally, DiffBind is used for ChIP-seq data, but I've seen it used for ATAC-seq as well. I don't see any issues with that. MACS can be used for...If the reads are adjusted for peak calling, what happens when I then pass the peaks and the BAMs to DiffBind? Wouldn't DiffBind quantify the peaks incorrectly since the BAMs and peaks do not really represent the same data

atac-seq diffbind macs2 macs peak finding

updated 8.9 years ago • igor

namespace (DiffBind) 13: "croi_count_reads" not resolved from current namespace (DiffBind) 14: "croi_count_reads" not resolved from current...namespace (DiffBind) 15: "croi_count_reads" not resolved from current namespace (DiffBind) 16: "croi_count_reads" not resolved from current...namespace (DiffBind) 17: "croi_count_reads" not resolved from current namespace (DiffBind) 18: "c…

diffbind read counting warning message chromatin atac-seq

updated 8.2 years ago • tgjohnst

I've been trying to use DiffBind for ATAC-seq data. I noticed that there is a large difference in differential accessibility depending on whether...or FALSE? Since I think this is likely related to FRiP, I'll post the scores below. ID Condition Replicate Caller Intervals FRiP A-1 A 1 counts 71007 0.44 A-2 A 2 counts 71007 0.44 A-3 A 3 counts 71007 0.3 A-4 A 4 counts 71007 0.29

diffbind atac

updated 6.9 years ago • paz2005

analyzing H3K27ac marks across multiple tissues. I have the following sample sheet (simplified) for DiffBind: | SampleID | Tissue | Factor | Condition | Replicate | |-------------------------|---------------|----------|---------------|-----------| | H3K27ac_adipose_r1 | adipose | H3K27ac | OtherTissues | r1 | | H3K27ac_adipose_r2...OtherTissue…

DiffBind

updated 10 months ago • lryrainche

I'm now running ATAC-seq differential analysis by DiffBind with peaks from MACS2. I have 10 samples from batch 3 and 20 samples from batch 5. How could I eliminate batch effect...and normalize them in DiffBind? Sorry, I'm quite new in this area. Thanks! Simon

diffbind atac

updated 8.6 years ago • niu.shengyong

span style="line-height:1.6">I am trying to reproduce the results of DiffBind for edgeR analysis.</span> A member of my research group did analysis with DiffBind and got nice results, whereas me...performing the edgeR separately could not get any results. DiffBind was called as follows: <pre> WNN_vs_WEN= dba.analyze(WNN_vs_WEN) </pre> According to DiffBind protocol: …

edger diffbind

updated 10.2 years ago • tonja.r

0, 0)">ifferential binding analysis of ChIP-Seq peak data </span>with DiffBind<span style="background-color:rgba(0, 0, 0, 0)">. I´m trying to use the code explained in the post: </span>https://support.bioconductor.org...p/71464/\#71501, because I don't have any replicate for my samples, and I know this is not the best way…

diffbind

updated 9.9 years ago • jvdelarosa

22:31 +0000 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: DiffBind loading Problem Dear Rory and Gordon, I would like to use DiffBind to compare my ChIPseq data in which I have two different...antibodies against the same transcription factor named Ptf1a (2 replicates for each antibody). I want to get undifferentiated peaks between the two…

Transcription ChIPSeq chipseq DiffBind Transcription ChIPSeq chipseq DiffBind

updated 12.0 years ago • Rory Stark

Hi, I used DiffBind for a collaborator who noticed that, contrary to his expectations, a particular region (which overlaps highly significant...Hi, I used DiffBind for a collaborator who noticed that, contrary to his expectations, a particular region (which overlaps highly significant (pvalue << 0.001) peaks from MACS2 in each replicate of condition Y) got a very low FDR when comp…

diffbind

updated 8.8 years ago • Silvia

I noticed a new vignette posted for DiffBind, which now includes an awesome option to plot data as a volcano plot.  I would love to use this, but I cant seem to...I noticed a new vignette posted for DiffBind, which now includes an awesome option to plot data as a volcano plot.  I would love to use this, but I cant seem to access this option in DiffBind even when updating the pac…

diffbind chipseq atac-seq rory stark

updated 8.8 years ago • andrew.gehrke

Hi all, I using DiffBind to compare WT vs Treatment ATAC-seq samples and I have two questions/problems regarding the DiffBind `` dba.report...with the same thresholds.  The input csv: <pre> SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks WT_1,hs,ATAC,WT,1,WT_1.bam,,WT_1.bed WT_2,hs,ATAC,WT,2,WT_2.bam,,WT_2.bed Treat_1,hs,ATAC...Treat_1.bed Treat_2,hs,AT…

diffbind differential binding analysis R report

updated 8.0 years ago • hlsz.laszlo

I'm now using DiffBind R package to conduct differential analysis for ATAC-seq dataset.  In this analysis, I want to compare each cell...I'm now using DiffBind R package to conduct differential analysis for ATAC-seq dataset.  In this analysis, I want to compare each cell type in two conditions, so I divided the general sheet into enclosed sheets with different cell names a…

diffbind atac-seq

updated 8.8 years ago • niu.shengyong

div class="preformatted">Hi, I'm Ken Tanaka. I'm currently interested in analyzing the DiffBind analysis by using the ChIP-seq data from Th2 immune cell samples. To be more specific, I would like to analyze this...GSE28292) by using DiffBind analysis. I have questions regarding the dba.count(). When I execute the dba.count(), it crashes. The bed data which I...from the problems regarding t…

DiffBind DiffBind

updated 12.7 years ago • kentanaka@chiba-u.jp

div class="preformatted">Dear list, I made a new samplesheet to use with DiffBind with this format: SampleID Tissue Factor Condition Replicate bamReads bamControl Peaks Contrl1 Neural K9 Resistant...more categories, or lower value for minMembers. ->My questions are: -What is the contrast for DiffBind (I added the input for each set of samples, and 2 b…

Alignment DiffBind Alignment DiffBind

updated 13.0 years ago • José Luis Lavín

Hello,  <span style="line-height:1.6">I am trying to use diffbind on paired end read data. I have done the following to get our proper peaks of interest ( we have technical replicates

diffbind

updated 10.2 years ago • jess.schust

<div class="preformatted">Hi, Your sample sheet shows the same filename for "Reads" and "Peaks", which is unlikely to be right. The "Peaks" file should be the output of the peak caller (the peaks that MACS called); the "Reads" file should be the aligned reads, i.e. the *input* to the peak caller (the output of the alignment stage). Let me know if that fixes the problem. It should give a…

DiffBind DiffBind

updated 13.1 years ago • Gord Brown

I am new to DiffBind. I have tried working with your test data and I have seen the tutorial online. I am facing some issues with DiffBind...getting any peaks using DEseq2 and EdgeR in my data. 3. Can we compare 4 different conditions in DiffBind? Is there an example available with you with more than 'Resistance' and 'Restrained' conditions? 4. For MACS2, do we need...to provide specificall…

DiffBind DifferentialPeakCalling

updated 3.9 years ago • Amandeep

div class="preformatted">Hi Igor- We avoided adding annotation to DiffBind because of the other packages that specialize in this. They don't take a DiffBind object directly, but you can always...Igor" <igor.dolgalev at="" nyumc.org=""> wrote: >Hello. > >I am getting started with DiffBind. I am really enjoying all the options >it provides. Unfortunately, it d…

Annotation ChIPpeakAnno DiffBind chipenrich

updated 11.4 years ago • Rory Stark

Hello, I am interested in using diffbind to perform differential expression analysis on some ATAC data. However, all I have is counts table for peaks (no beds...Hello, I am interested in using diffbind to perform differential expression analysis on some ATAC data. However, all I have is counts table for peaks (no beds or bams) and a meta table with the sample names and conditions they…

diffbind ATACseq ATAC counts differential analysis

updated 6.8 years ago • pgontarz

Dear Dr. Stark, The following question has been asked before regarding error in dba.analyze step of diffBind when the contrast is set up for samples with no replicates. Obviously I should be comparing samples with multiple...replicates but while I wait for more data from the sequencer it will be great if I could implement DiffBind for no replicates...operator is invalid for atomic vectors__ I…

diffbind

updated 10.8 years ago • danishm20

<div class="preformatted">Hello Igor- This feature has just been added to the upcoming release of DiffBind. It is part of Bioconductor 2.14, due to be released 14 April, and currently available in the Development branch. dba.plotPCA has been reworked to use xyplot() from the lattice package. It now automatically draws a legend alongside the plot, and there is a new parameter, labels, for …

DiffBind DiffBind

updated 11.8 years ago • Rory Stark

<div class="preformatted">Hi Anna- I've shared the Dropbox location containing all the reads for the vignette with you. I do want to ask what version of DiffBind you are using (perhaps send a sessionInfo() output?). The latest version (Bioconductor 2.13/DiffBind 1.8) has substantially new code for dba.count (using much less memory) - you may want to check this out. Also, if memory is an …

DiffBind DiffBind

updated 12.3 years ago • Rory Stark

Hi All, I'm analyzing ATAC-seq data and use `` MACS2 `` for peak calling and `` DiffBind `` for occupancy and affinity analysis. In occupancy analysis when I try to find peaks that are unique to one group...Hi All, I'm analyzing ATAC-seq data and use `` MACS2 `` for peak calling and `` DiffBind `` for occupancy and affinity analysis. In occupancy analysis when I try to find peaks that are uni…

atacseq diffbind

updated 7.3 years ago • gtechbio

however, I need help at this point. My goal is to use pre-normalised data (e.g. using MAnorm) as DiffBind input so that later I can create contrast list (dba.contrast), reports (dba.report) and plot (dba.plotXYZ). Question...output (MAnorm\_result\_commonPeak\_merged.xls) obtained after MAnorm normalization as an input for DiffBind? Any help or recommendation is appreciated.  …

MAnorm diffbind normalization chipseq

updated 5.2 years ago • ajeet

Hi all, I am new to Diffbind and following the workflow from the handbook: https://bioconductor.org/packages/devel/bioc/vignettes/DiffBind...samples have 0 counts for all genes. check the counting script. what is it that went wrong ? my Diffbind version is (DiffBind_3.4.11) Thanks

peakfiles diffbind HMMRATAC

updated 3.6 years ago • jonathanho1989

Hi community! I am providing to Diffbind a genomic region list to be analyzed (not peaks, just regions of interest). Although the results are good, I want to avoid...Diffbind to merge some of the regions that actually overlap. Can I do that? I have trying so far with no success. Any help?   Thanks

diffbind chipseq

updated 9.2 years ago • sergio.espeso-gil

I have a couple questions regarding the dba.plotPCA function in diffbind. The relevant figures are here: <https://www.dropbox.com/sh/co3oywz8r745m8o/AACouCCG1q9UEyASR5igqXX9a?dl...I have a couple questions regarding the dba.plotPCA function in diffbind. The relevant figures are here: <https://www.dropbox.com/sh/co3oywz8r745m8o/AACouCCG1q9UEyASR5igqXX9a?dl=0> I've been …

diffbind news

updated 7.1 years ago • jingyaq

Hi all, I have a fairly complex ChIP-seq experiment with lots of treated/untreated groups, 2 replicates each. All the 'replicate 1s' were generated together, separately to the 'replicate 2s' and I can see that that effect...in the final matrices, to the extent that it's stronger than my treatment effects. I'd like to use DiffBind's blocking function to account for that. The contrasts I wish to …

diffbind batch effect

updated 9.5 years ago • Jon Manning

Hello, I'm trying to run DiffBind on my CUT&RUN data to get the differentially bound peaks between two conditions (DMSO and inhibitor). In sample_sheet.csv...I only have the four samples I want to compare, two replicates each, and I'm running the following analysis: ```r samples_file=read.csv("sample_sheet.csv", header=T) Diff_dba=dba

DiffBind DESeq2

updated 2.1 years ago • Miquel

student trying to analyse Chip-seq data generated in my project but I'm loosing it to use properly DiffBind package even if I read several times the manual. To illustrate my work : Chip-seq on flies: * 3 Lineages (A, B and C) x 3 treatments...nbsp;   In treatment CO, difference between A and B , B and C... If I understand the Diffbind package usage : 1. I imported data …

diffbind chip-seq R

updated 7.3 years ago • pierre.marin

style="line-height:1.6">heat map</span><span style="line-height:1.6"> plot which generation by diffBind.</span> <span style="line-height:1.6">When we employing diffBind on those commands, it will generate </span>heat map

diffbind

updated 10.8 years ago • yijing.su

I'm trying to use DiffBind for re-analyses of some data. The only files that are changed from my previous run of DiffBind are the peak files from...MACS2. They are still in the same format as before. Previously I was able to run Diffbind and analyse this same dataset without errors. However, now when I try the very first step of DiffBind (ta <- dba(sampleSheet

diffbind

updated 10.6 years ago • mm2489

Hi, I am new to diffbind and have a question about the GRange report generated from dba.report() function. in the demonstrated report (tamoxifen.DB

diffbind

updated 3.6 years ago • jonathanho1989

to mouse and drosophila genome separately. And now I am trying to get normalization factors for each replicate using DiffBind (v. 3.8.3), which I would like to use for differential peak analysis as well as scaling bigwig files...Qn1:* From what I can gather, in DiffBind, by including the spikein bam filles in the Spikein column of sampleSheet, I have the option to use the spikein library...it. T…

DiffBind SpikeIn Normalization ChIP-seq csaw

updated 3.1 years ago • spg

Hi community! I am subsampling input control data for DiffBind analysis to test something. I have merged first input files by using samtools merge and then later samtools view...s "percentage of subsampling"   When I am trying to run DiffBind, then I get this error: 'subsampled\_input.bam'  does not appear to be a BAM file (bad magic number) Any ideas? I am browsing...in in…

diffbind samtools

updated 8.8 years ago • sergio.espeso-gil

Hi, Dr Stark. In the [Question: diffBind: differentially bound sites are highly different between using EDGER and DESEQ2](https://support.bioconductor.org...full library size, total number of reads in BAM/SAM/BED file, instead of the peak count)** in Diffbind project. Best wishes Guandong Shang

diffbind

updated 5.2 years ago • shangguandong1996

not significant over input). In this case I would assume this peak has been brought through to the DiffBind consensus set because it is in 2 or more samples of timepoint A or B. My question is is it okay that this peak is not significant...over input at that timepoint but is significant in the DiffBind? I know DiffBind and MACS2 are different methodologies. How does DiffBind take into account the…

DiffBind MACS2

updated 5.4 years ago • ep15587

After reading the vignette (https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf) I still have doubts on how grey lists are derived in `DiffBind` ? Could someone please explain

DiffBind

updated 4.6 years ago • Alexandre

Hi, I'm trying to understand what exactly is done by the dba.plotPCA function from DiffBind. I tried to reconstruct the plot generated by dba.plotPCA but for some reason I get a different plot. Could you...by the dba.plotPCA function? Thanks! Razvan   Here is what I've tried (I used DiffBind\_1.14.6): library(DiffBind) data(tamoxifen\_peaks) dba.plo…

diffbind

updated 10.1 years ago • r.chereji

Hi, In the current version of DiffBind what are the steps for indicating that PE data is being used? Thank you. Rob &nbsp

diffbind paired-end reads

updated 5.2 years ago • rbronste