6 votes
Accepted

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
4 votes
Accepted

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
  • 19.6k
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
  • 3,311
3 votes

Detecting broad peaks in sRNA-seq data

The sure why any software should be confined to only broad peaks, but there is two packages that should do what I thing you have in mind. Just to clarify, for smallRNAs peak detection is sometimes ...
Sebastian Müller's user avatar
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

Finding peaks and estimating cell population sizes in multi-dimensional flow cytometry data

Automated gating methods are gaining popularity over manual and time consuming analysis in say FlowJo, you should take a look at the openCyto bioconductor package this is a framework which builds on ...
Matt Bashton's user avatar
  • 1,069
2 votes

Finding peaks and estimating cell population sizes in multi-dimensional flow cytometry data

There are quite a few algorithms developed for the automatic classification of multidimensional flow cytometry data, you can see a (not so recent?) review here: http://www.nature.com/nmeth/journal/v10/...
Leo Martins's user avatar
2 votes

What is the required input peak file format for IDR (Irreproducible Discovery Rate)

As mentioned in the IDR readme on usage, there are examples in the IDR github repository here. Here's one of them: ...
gringer's user avatar
  • 14.1k
2 votes

annotation using ChIPseeker package error

that was solved by changing seq level: ...
Mariam's user avatar
  • 115
1 vote

Gene list from eclip-seq .bed files

As someone who works with eCLIP data from ENCODE, I think I can help out. You need to think of this more similar to ATAC or RNA-Seq, whereby you actually get a counts matrix, normalize that, and then ...
YogiOnBioinformatics's user avatar
1 vote

Separating peaks of chip-seq with specific length

You can use rtracklayer from R bioconductor to import it, filter and do much more stuff, i use the code from this blog for ...
StupidWolf's user avatar
  • 1,688
1 vote
Accepted

Separating peaks of chip-seq with specific length

You can do it by awk. awk -v OFS="\t" '{ if ( ($3-$2) >= 500 && ($3-$2) <= 1000) { print } }' in.bed > out.bed Assuming there is no ...
geek_y's user avatar
  • 321
1 vote
Accepted

How to calculate the number of peaks that are upstream/downstream of some other peaks

You can use windowBed from bedtools with -c if you just want counts. Or use -wa -wb and then ...
geek_y's user avatar
  • 321
1 vote

differential analysis of chip-seq data

For sharing, you can test the proportion of overlapping peaks using bedtools intersect or the find.overlap function in ...
Phoenix Mu's user avatar
1 vote

Hypergeometic test for the overlap of two set of genomic intervals (e.g. from Chip-seq data)

Just to make sure, I took a quick look at chippeakanno, and it uses a hypergeometric test for gene enrichment, not necessarily overlap of two chip-seq results. As you mentioned, you can imagine in ...
Phoenix Mu's user avatar
1 vote

How to make Venn diagram for the Macs peak calling output of two data sets?

Venn diagrams can be helpful, but for peak calling they can be somewhat misleading. This topic is addressed in the DiffBind documentation, in the "Comparison of occupancy and affinity based analyses" ...
James Hawley's user avatar
  • 1,384
1 vote

How to make Venn diagram for the Macs peak calling output of two data sets?

Check out the tool Intervene. It's exactly designed for this. Github link.
cat's user avatar
  • 19
1 vote
Accepted

How to get the intersection of peaks after peak calling using MACS2?

bedtools intersect with multiple files after -b performs pairwise intersections between -a ...
James Hawley's user avatar
  • 1,384
1 vote
Accepted

Peak-calling using homer

You just need to strip the / from $d, for which there are a number of options: ...
Devon Ryan's user avatar
  • 19.6k

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