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Questions tagged [chip-seq]

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3
votes
0answers
22 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
29 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
71 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
16 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
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1answer
34 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
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1answer
55 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
19 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
69 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
59 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
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0answers
39 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
28 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
45 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
602 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
43 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
444 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
296 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
473 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
0answers
392 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
37 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
363 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 ...
6
votes
1answer
469 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
402 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
52 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
168 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
356 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
261 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
200 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
2k 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 ...