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10 votes

When to account for the blacklisted genomic regions in ChIP-seq data analyses?

Aside: Cross-correlation is largely meaningless, regardless of what some of the ENCODE folks might argue. When we process our DEEP samples we don't even look at that value. Regardless, if you're ...
Devon Ryan's user avatar
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10 votes
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How are MACS2's narrow peak and broad peak algorithms different?

The key function is call_broadpeaks: The description attached to the function says: This function try to find enriched regions within which, scores are ...
Daniel Kim's user avatar
7 votes
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variant calling on ChIP-seq style data: samtools mpileup with minimal filters

I used this in the past for ChIP-seq data and it generated SNVs: ...
burger's user avatar
  • 2,199
7 votes
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Merging sequencing data for ChIP-seq experiments

I don’t think it matters. Both are easy to merge (BAM via samtools merge, and (gzipped) FASTQ via cat), and neither method has ...
Konrad Rudolph's user avatar
6 votes
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Hypergeometic test for the overlap of two set of genomic intervals (e.g. from Chip-seq data)

There is no such thing as a hypergeometric test, at least in statistical textbooks. It's a fisher test based on hypergeometric distribution. If it is chip-seq for the same target, i.e biological ...
StupidWolf's user avatar
  • 1,688
5 votes

variant calling on ChIP-seq style data: samtools mpileup with minimal filters

Another approach is htsbox. You can get a candidate list with: htsbox pileup -Cvcf ref.fa -q20 -Q20 -s5 file.bam > out.vcf Here, ...
user172818's user avatar
  • 6,535
5 votes

Given a transcription factor, what genes does it regulate?

MSigDB has a collection (C3:TFT) of gene sets corresponding to transcription factor targets. Harmonizome has functional terms for genes extracted from over a hundred publicly available resources.
burger's user avatar
  • 2,199
5 votes

Converting Chip-seq fastq format ({$x_k$} list of seq segments) to genome browser {sequence $x_i$, count-number $y_i$} format

I have no idea about what you are actually trying to achieve, but getting these browser tracks is simple. First you align your fastq files to a reference genome, e.g. with ...
alderaan_shot_first's user avatar
4 votes
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Macs2 peak calling?

Your original command without --nomodel --extsize ... is probably the most accurate. This warning stems from a time when reads were much much shorter and likely ...
Devon Ryan's user avatar
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4 votes

Input normalization in ChIP-seq

I strongly suggest that you not try to come up with your own package for this when things like CSAW already exist in bioconductor and provide a number of useful ...
Devon Ryan's user avatar
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4 votes

Chip-Seq data description

That's a fastq file, you will want to align it to the genome, call peaks, and then use something like MEME to determine binding motifs.
Devon Ryan's user avatar
  • 19.6k
4 votes

Given a transcription factor, what genes does it regulate?

In general, there is two options to identify targets for transcription factors: experimental (ChIP-seq) and sequence-based predictions. TF binding from experimental data The are multiple projects ...
Michael Schubert's user avatar
4 votes

Given a transcription factor, what genes does it regulate?

iRegulon takes a sequence-based approach to finding transcription factor targets. There's a Cytoscape app that you can use to find the regulators of a given gene list, or the targets of a particular ...
sjcockell's user avatar
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4 votes
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Where to download JASPAR TFBS motif bed file?

You could make your own such file with FIMO, the JASPAR MEME files available via the MEME download site, and your genome build of interest (per-chromosome FASTA files from UCSC goldenpath, say), e.g., ...
Alex Reynolds's user avatar
4 votes
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Occupancy of TFs with the target genes

I would ignore peak calling for this and instead compute enrichment of ChIP/input for the genome (e.g., with deepTools or presumably homer) and then plot it for the genes of interest individually (e.g....
Devon Ryan's user avatar
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3 votes
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Is there any way to align ChIP-seq reads to telomeres?

This paper https://www.biorxiv.org/content/10.1101/728519v1.full examines the mapping of some human telomeric sequences, and indicates that there is something like 130kb missing at the telomeres in ...
Jay Moore's user avatar
  • 1,012
3 votes

Where are .motif files from homer knownResults?

I have provided a solution in Biostars: If you edit the file findKnownMotifs.pl and move the call to printMotif to come before ...
malcook's user avatar
  • 191
3 votes

determine if ChIP-seq peaks are broad or narrow

I'd say mostly this is a question of understanding the underlying biology and the relevant literature. If it is not known in the literature whether a mark is peaky or broad, evidence might come from ...
Ian Sudbery's user avatar
  • 3,321
3 votes

Merging sequencing data for ChIP-seq experiments

For ChIP-seq it shouldn't really matter. But do be aware that by default, samtools merge retains read group information (the @RG ...
Sarah Carl's user avatar
2 votes

Merging sequencing data for ChIP-seq experiments

Agree with the others that it doesn't really matter. One thing to note though - if you're deduplicating your BAM files (you probably should for ChIP-seq data), make sure that you do this after merging....
ewels's user avatar
  • 291
2 votes

Score predefined ChIP-seq peaks with MACS2 or equivalent

You could try setting a high p-value threshold when you're calling peaks to retain the "non-significant" values. Something like: ...
James Hawley's user avatar
  • 1,384
2 votes
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Integrative analysis of omics studies using machine learning

The steps you describe are correct. For step 2 it is usually normalized to mean 0 and variance 1. However the "machine learning" part is important. Having several samples being technical replicates ...
llrs's user avatar
  • 4,713
2 votes

Biological replicates on Chip-seq Transcription factor data

This question is somewhat generic, so a generic answer is that ENCODE has a Transcription Factor ChIP-seq Data Standards and Processing page that can give you a useful starting point. For TF ChIP-seq ...
James Hawley's user avatar
  • 1,384
2 votes

Biological replicates on Chip-seq Transcription factor data

You could first look at the degree of correlation between the two replicates - what proportion of peaks are shared between the two, versus peaks found in one sample only? This will give an idea of ...
Jay Moore's user avatar
  • 1,012
2 votes

Tag density plot form chip or atac seq data

You can use Homer to retrieve tag densities, quoting from their manual: Calculating ChIP-Seq Tag Densities across different experiments annotatePeaks.pl is [...
haci's user avatar
  • 4,142
2 votes

Aligning ChIP-Seq reads to repeats for downstream peak analysis

This is very good question, but as far as I know there really isn't a good answer. I will attempt to provide some comments and tips. However, I'm trying to do similar with a dataset which may ...
fridaymeetssunday's user avatar
2 votes
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How to visualize called narrowPeak files in UCSC Genome browser or IGV?

I think you might have changed the separator (or at least have some kind of inconsistency from the required format) for your file. Note that peak output files from MACS2 are variants of BED files. It ...
story's user avatar
  • 1,573
2 votes

How to visualize called narrowPeak files in UCSC Genome browser?

Headers should not contain tabs: track type=narrowPeak name="Somite narrowPeak" description="Somite narrowPeak" Ensure that you have NO tabs on ...
Devon Ryan's user avatar
  • 19.6k
2 votes

annotation using ChIPseeker package error

that was solved by changing seq level: ...
Mariam's user avatar
  • 115
2 votes
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chipseeker annotation issue

I had a similar case just recently. The tssRegion argument ChIPseeker is used to define what is considered a promoter, which is frequently the question at hand. ...
PPK's user avatar
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