Questions tagged [chip-seq]

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differential analysis of chip-seq data

I have several sets of chip-seq data. I called the peaks using Macs2. I am pretty new to the field and I will appreciate any help. I wanted to annotate the peaks and see which peaks are shared between ...
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12 views

How to calculate overlapping between different chip-seq peaks

I have 3 sets of data for peaks called by Macs2 as below: 1-DNA methylation 2-Chip-seq (repression marks) 3-Chip-seq (activation marks) I need to show how many peaks in DNA methylation have the same ...
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2answers
52 views

Hypergeometic test for the overlap of two set of genomic intervals (e.g. from Chip-seq data)

Suppose I have done two Chip-seq experiments. Now after the bias correction step such as MACS2, I get two set of genomic intervals (or peaks, as what is usually called) that corresponds to each of the ...
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1answer
23 views

marge the matrix from computematrix of deeptools

I have several matrix from computematrix of deeptools. I need to merge two of them using "computeMatrixOperations cbind -m input1.mat.gz input2.mat.gz -o output.mat.gz" but I am running to error "/...
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2answers
36 views

How to make Venn diagram for the Macs peak calling output of two data sets?

I have two outputs of macs2 peak calling for two of my data sets. I wanted to plot the Venn diagram to see how many peaks are shared. I mainly work on Unix/Linux. Do you know any way that I can have ...
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1answer
43 views

plot correlation between several bam files

I have several mab files from medip-seq. they supposed to be replicates and I have to draw their correlation. First I used multiBamSummary from deeptools to merge all the bam files based on bi/bed. ...
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1answer
42 views

what is the concept of N-channel geneChip?

I can understand two-color and one-color(Channel) gene chip; but there is another type of gene-Chip called "N-channel chips" ; I do not know how can several (> 2) samples be hybridize in one chip. I ...
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1answer
38 views

How to get the intersection of peaks after peak calling using MACS2?

I have following 5 narrow peak files after peak calling. K14_peaks.narrowPeak K15_peaks.narrowPeak K16_peaks.narrowPeak K3_peaks.narrowPeak K8_peaks.narrowPeak I ...
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30 views

Pol_II genome wide occupancy analysis

Paper Figure 1G So in this figure they are analysing the Pol II occupancy in Control,PAF1 KD and LEO1. I have similar data.I would like to know how do I perform this global Pol II occupancy which ...
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23 views

When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted original BAM files?

I have called peaks using MACS2 and now I'm trying to run ChIPQC bioconductor package. Can someone please tell me should I use sorted BAM files or unsorted original BAM files? I have created sorted ...
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1answer
156 views

How to visualize called narrowPeak files in UCSC Genome browser or IGV?

I have called peaks using MACS2. Then I got a narrowPeak file like this. ...
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20 views

How to decide the parameters and parameter values when running ChIP-seq Peak Calling for H3K27ac data in MACS?

I have alignment data in SAM files from ChIP-seq analysis for H3K27ac mark. I need to call peaks using MACS2. But I'm having issues with selecting parameters and values of the parameters. I will be ...
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23 views

Find covariation of different DNA-binding protein binding between two conditions

I have ChIP-seq data of RNAPII and two other factors which we think follow RNAPII during transcription in two different conditions, and I'd like to show that the genes that lose RNAPII also lose the ...
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1answer
111 views

Tag density plot form chip or atac seq data

I m quoting this paper , figure B where they write "B) Violin plots for the normalized ATAC-seq tag density for all peaks within the indicated OC/CO groups at the indicated time points. Data were ...
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2answers
79 views

Is there any way to align ChIP-seq reads to telomeres?

I know that telomeres are highly repeated sequences, but is there any way to retain any reads that map to these regions (on HG38)? I recently managed to find some protein binding to centromeres, ...
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1answer
43 views

RPGC normalisation creates artefacts at centromere

I am studying ChIP-Seq data in HeLa cells and I've started using the RPGC normalisation of deepTool's bamCoverage. MACS2 also uses this normalisation for its peak calling. I am seeing a large number ...
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1answer
162 views

How to convert a .fastq chip-seq file into a wig/bigwig track and how to extract chip-seq peaks?

I have a reference .fasta file and a raw .fastq file with chip-seq data. I am trying to create a bigwig track from the and .fastq and .fasta ref file of the raw signal. Then I would like to do some ...
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1answer
148 views

Error: package or namespace load failed for 'ChIPseeker'

How do I solve the problem of loading the bioconductor Chipseeker package? I have installed in the following way and I having an error while loading it and I do not know why. ...
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0answers
20 views

Chip seq sample sequencing depth issue

What is the optimum depth needed to get enrichment signal in chip seq data? The samples I have is like for the control INPUT samples the depth is around 40-50 million reads where as the IP samples ...
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2answers
190 views

Biological replicates on Chip-seq Transcription factor data

I have 2 biological replicates for chip-seq transcription factor data and I have applied macs2 peak calling for each replicate separately. How can i make use of the biological replicates to extract ...
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1answer
68 views

Occupancy of TFs with the target genes

The occupancy of SMARCD3 in the target genes listed below. I want to see average, normalized ChIP-seq signal at the promoter proximal region (1000bp upstream and downstream of the TSS). I have 4 ...
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61 views

How can I convert Affymetrix microarray data to bedgraph format?

I've previously asked a different question about the ChIP-chip microarray data that I'm working on. I'm new to this so I'm sorry for asking here again. I have .CEL files and I'm using the Affy ...
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1answer
55 views

How to convert ChiP-seq track in .bam file format into an array at fixed bin resolution?

Is there a out of the box to convert a .bam file to a .wig file at specific resolution/bin size? I was thinking to use igvtools, but I am not sure how it works: ...
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1answer
74 views

Score predefined ChIP-seq peaks with MACS2 or equivalent

I have performed peak calling on a number of separate ChIP-seq experiments and would like to harmonise the peaks from each of the experiments in order to convert my data into a matrix for further ...
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1answer
863 views

Integrative analysis of omics studies using machine learning

I would like to use public omics datasets (ChIP-seq, RNA-seq, and ATAC-seq) from different studies to do an integrative analysis as follow: Normalise samples, within each type of omics, from ...
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0answers
63 views

peakranger bcp segmentation fault

I'm running into a segmentation fault running peakranger's bcp on Arch Linux. Binaries were compiled from source just today. Any idea how I can prevent this? ...
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2answers
654 views

Input normalization in ChIP-seq

If I subtract input counts from ChIP counts (for every gene, since I have one peak per gene) I get negative values for most genes. This makes sense to me, because (as can be seen in the figure) input ...
3
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1answer
427 views

determine if ChIP-seq peaks are broad or narrow

Is there a method to determine if the peaks are broad or narrow? ENCODE provides some guidelines: Although those cover common histone marks, there are many others. If you are using one of the ones ...
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1answer
728 views

Macs2 peak calling?

I have paired end ChIP-seq data with 101 bp and 2 biological replicates for each one. I have done peak calling with macs2 but I have some questions about it. I also faced with an warning: WARNING @...
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0answers
514 views

What are phantom peaks in ChIP-seq?

I've seen two uses of this term that seem to refer to completely different phenomena. Is my understanding correct? In Jain et al. "Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-...
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0answers
58 views

How long does it typically take to call peaks via `phantompeakqualtools`?

I'm running the script run_spp_nodups.R from phantompeakqualtools. The input is a pair of BED 3+3 ("tagalign") files that are ...
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1answer
479 views

Aligning ChIP-Seq reads to repeats for downstream peak analysis

This is a brief question regarding the above. I have previously used bowtie to map reads from paired-end ChIP-Seq sequencing, then used the positions for peak-calling. However, I'm trying to do ...
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1answer
725 views

Where to download JASPAR TFBS motif bed file?

I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment. I am looking for a database that has BED Files ...
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2answers
535 views

Where are .motif files from homer knownResults?

I have been using homer's findMotifsGenome.pl, but with my new version (v4.9.1) of homer I don't get ...
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1answer
57 views

Chip-Seq data description [closed]

I have the following Chip-Seq data and could not found a description of it. Can you help me with it? More, I would like to find out the order of the nucleotides in binding regions; that is, what ...
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4answers
194 views

Given a transcription factor, what genes does it regulate?

I have a list of transcription factors and I am interested in finding out which which genes might be transcribed as a result of the formation of transcription factor complexes with that transcription ...
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1answer
468 views

When to account for the blacklisted genomic regions in ChIP-seq data analyses?

We have heard in the group that it is important to keep track of and to filter artifact regions when analysing data from functional genomics experiments, especially ChIP-seq. Here, we have seen ...
7
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3answers
367 views

Merging sequencing data for ChIP-seq experiments

I need to merge sequencing data from different sequencing runs but for the same ChiP-seq library (HiSeq 2000). Are there any potential advantages or disadvantages when merging files at .fastq or .BAM ...
7
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2answers
228 views

variant calling on ChIP-seq style data: samtools mpileup with minimal filters

I am running samtools mpileup (v1.4) on a bam file with very choppy coverage (ChIP-seq style data). I want to get a first-pass list of positions with SNVs and their frequency as reported by the read ...
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1answer
3k views

How are MACS2's narrow peak and broad peak algorithms different?

The peak calling tool MACS2 can call peaks in either narrow peak mode (for focused signals like transcription factor ChIPseq) or broad peak mode (for more defuse signals, like certain histone ...