Questions tagged [chip-seq]

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Problems about value log2(IP/Input) less than zero in ChIP-seq?

I have a question about the normalization for ChIP-seq. I used CPM to normalize my bam files of each IP and Input. Then I calculate the coverage of gene bodies for all genes on the genome. I have WT ...
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1answer
27 views

How to interpret track height in Chipseq?

I recently received some .bigwig files from a chipseq experiment. I loaded the files into IGV. The interpretation is rather intuitive. My question is the following: What exactly do the track heights ...
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18 views

How to identify specific motif for chip-seq data

For chip-seq data, I had analyzed the samples until motif discovery using both cluster profiler and Homer for each histone mark. I was wondering what is the efficient method to determine if each GO ...
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1answer
20 views

chipseeker annotation issue

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1answer
23 views

Chip-seq down-sampling problem

Control sample chip read stat ...
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10 views

How to annotate ChIP peaks base on NCBI sequence name?

I have chip-seq peaks based on NCBI genome which looks like the following: ...
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1answer
127 views

annotation using ChIPseeker package error

I have differential binding sites object obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error: Error in (function (classes, ...
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1answer
21 views

Extracting concatenated metadata from a column in R

I've downloaded some ChIP-seq data from www.chip-atlas.org and I want to use this to conduct some enrichment tests with genomic regions from my experiment. The .bed file generated by that website is ...
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1answer
21 views

How can I add for several bed files the header : track type=narrowPeak name=“narrowPeak” preferably in python ,can handle with R

I want to create custom tracks from these files I can add the line : track type=narrowPeak name=“narrowPeak” manually by opening it with text editor: track type=narrowPeak name=“narrowPeak” but I ...
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1answer
48 views

How to visualize called narrowPeak files in UCSC Genome browser? [closed]

I have this file: and I get this error I googled and found this solution but it still doesn't work and I get this error Error File 'GSM2797523_FOXA2_IDR0.02_narrowPeak_try.bed' - line 1 of custom ...
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17 views

Why does the ENCODE chip-seq pipeline discards reads with a hard-clipped alignment?

Hard-clipped alignments are alignments in which one or both the ends are clipped AND map to other genomic coordinates. As you may know, BWA-MEM reports hard-clipped alignments as supplementary. ENCODE'...
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2answers
66 views

Recommended coverage depth for ChIP Seq (H3K9me3 )

According to ENCODE recommendations For broad-peak histone experiments, each replicate should have 45 million usable fragments According to my understanding, a usable fragment means a uniquely ...
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0answers
15 views

Methods to analyze MeDIP-seq data

I have MeDIP-seq data. I have 6 groups with 15 replicates and a total of 90 human samples. I am trying to choose the best method to analyze them. I would highly appreciate if you can give me your ...
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2answers
216 views

Installing HiC-Pro issues

I am setting up a HiChIPseq pipeline, but installing software necessary for the HiC side of things has been unbecoming. Both my PI and I have tried to install Hi-C Pro onto our Mac Pro that we use as ...
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2answers
30 views

Separating peaks of chip-seq with specific length

My data contain several chip-seq results. I have the peaks called by MACS2.I wanted to only look at those peaks that their size is e.g 500bp to 1000bp. How can I separate those peaks efficiently? I ...
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1answer
22 views

How to calculate the number of peaks that are upstream/downstream of some other peaks

I have 3 histone marks,I have used Macs2 for peak calling and diffBind to analyze the peaks. I was wondering if you know any way to calculate the peak numbers of one specific histone mark that occur ...
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1answer
32 views

DiffBind, diffferentially binding site

I have data for 3 histone marks (2 for silencing and 1 for activation) each mark has three replicates. when I run the diffBind package I have three contrast: ...
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3answers
56 views

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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2answers
182 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
61 views

merge 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
79 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
93 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
50 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
144 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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34 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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1answer
75 views

When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted 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 BAM files? I have created sorted BAM files ...
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1answer
599 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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1answer
39 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
285 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
90 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, ...
2
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1answer
89 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
390 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
300 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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2answers
381 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
79 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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0answers
100 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
81 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: ...
1
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1answer
89 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
879 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
77 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
947 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
582 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
975 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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1answer
730 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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68 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
571 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
1k 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
684 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
61 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
220 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 ...