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Questions tagged [chip-seq]

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2
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1answer
73 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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11 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? ...
0
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2answers
111 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 ...
2
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1answer
61 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 ...
3
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1answer
123 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
128 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
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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 ...
2
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1answer
192 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 ...
5
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1answer
162 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 ...
3
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2answers
220 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
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1answer
47 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 ...
5
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4answers
125 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 ...
8
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1answer
177 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 ...
6
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3answers
120 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 ...
6
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2answers
136 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 ...
6
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1answer
968 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 ...