Chip-Seq : how to test if several genomic regions are enriched in histone marks · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Chip-Seq : how to test if several genomic regions are enriched in histone marks

Hi,

Simple question but I'm a little bit new in the epigenetic world. So I've a bunch of very small region (~100b) and I want to know if these regions are enriched in histone marks.

My idea was to use ENCODE data and to intersect them with my input regions, to compute a score and to perform like a randomization test by picking random small region, and comparing random score with my input score. But do I have to use the signal bigwig file (bigWigAverageOverBed can compute the average score for a region from a bigwig file )? or the peak file?

Other ideas?

Thanks

encode enrichment chip-seq peaks bigwig

• 3,160 views • link

updated 4.7 years ago by Ram

• written 12.1 years ago by Nicolas Rosewick

1 answer

Have a look at Genometricorr and GAT packages, they might point you in the right direction.

• 0 views • link

updated 7.1 years ago by Ram

• written 12.1 years ago by dariober

Log in to answer this question.

More posts like this

Define enhancer regions
written 2.6 years ago by Faiza •

Hi! I need to get enhancer regions from publicly available data e.g ENCODE. Encode contain Histone marks bigwig file which is Signal p value and …
Histone marks enrichment analysis
written 5.0 years ago by gspirito •

Hello everyone, here's my question: I have a bed file of human genomic coordinates (hg19), and I would like to know whether ChIP-seq peaks for …
Identify genes with chip signal > input prior to peak calling
written 7.5 years ago by SciDuck •

Hi everyone, I need to identify which genes in my histone ChIP-seq experiment have greater signal for chip than for input (enrichment). I have made …
what do negative values from bigWigAverageOverBed output mean?
written 9.9 years ago by AB

Hi, This might seem basic, but I have a bed file with promoter regions I am interested in and Bigwig files from my ChIP-Seq experiment …
Align HTS on microsatellite
written 10.5 years ago by Nicolas Rosewick

Hi, I've a bunch of HTS data enriched for specific microsatellite (MS) regions. My idea was to create a bwa index based on these microsatellite …
bigwig to peak
written 12.1 years ago by Nicolas Rosewick

Hi, I've a bigwig containing a chip-seq signal for a histone mark (H3K4me1) and I want to produce a bed file containing the peaks (the …
bigwig : peak distance from specific genomic region
written 12.1 years ago by Nicolas Rosewick

<p>Hi,</p> <p>I've a bigwig representing chip-seq peaks and I've a bed file containing a bunch of small genomic region (~100b) . How can I intersect …
Genomic positions enrichement in enhancer
written 12.1 years ago by Nicolas Rosewick

Hi, I've a bunch of genomic positions and I want to check if these positions are enriched in TF binding sites or enchancer ? My …
Pick random position from specific genomic regions
written 12.3 years ago by Nicolas Rosewick

Hi, I've a bed file containing several region of interest and I want to pick randomly N positions in these regions. I know that "bedtools …
Bigwig To Wig On Galaxy
written 13.3 years ago by spacemorrissey

<p>I would like to use the Aggregate Datapoints tool in Galaxy to calculate the average signal score over a number of intervals. Unfortunately this tool …