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Questions tagged [chip-seq]

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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
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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
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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
201 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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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
243 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
171 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
264 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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244 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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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
261 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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279 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
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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
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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
157 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
255 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 ...
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3answers
168 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
171 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
1k 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 ...