Questions tagged [chip-seq]
The chip-seq tag has no usage guidance.
49
questions
0
votes
1answer
17 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 ...
0
votes
1answer
24 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 ...
0
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0answers
13 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'...
0
votes
1answer
18 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 ...
0
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0answers
10 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 ...
0
votes
2answers
30 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 ...
0
votes
2answers
26 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 ...
2
votes
1answer
18 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 ...
1
vote
1answer
23 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:
...
0
votes
2answers
36 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 ...
0
votes
0answers
16 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 ...
0
votes
2answers
75 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 ...
1
vote
1answer
33 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 "/...
0
votes
2answers
44 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 ...
1
vote
1answer
66 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. ...
1
vote
1answer
43 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 ...
1
vote
1answer
65 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 ...
0
votes
0answers
33 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 ...
1
vote
1answer
36 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 ...
1
vote
1answer
289 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.
...
0
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0answers
22 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 ...
4
votes
0answers
34 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 ...
0
votes
1answer
163 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 ...
2
votes
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, ...
2
votes
1answer
60 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 ...
0
votes
1answer
242 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 ...
0
votes
1answer
190 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.
...
1
vote
0answers
21 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 ...
1
vote
2answers
258 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 ...
3
votes
1answer
73 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 ...
1
vote
0answers
66 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 ...
1
vote
1answer
58 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
vote
1answer
78 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 ...
3
votes
1answer
869 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 ...
1
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0answers
65 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?
...
2
votes
2answers
732 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
votes
1answer
471 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 ...
5
votes
1answer
797 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 @...
1
vote
1answer
585 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-...
1
vote
0answers
62 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 ...
3
votes
1answer
508 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 ...
7
votes
1answer
811 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 ...
4
votes
2answers
591 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 ...
-3
votes
1answer
60 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 ...
7
votes
4answers
204 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 ...
10
votes
1answer
512 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
votes
3answers
413 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
votes
2answers
243 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 ...
8
votes
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 ...
