Questions tagged [homer]

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2
votes
1answer
52 views

Pausing index calculation

I have Pol_II data for Ctrl vs Knockout condition with two replicates each. I want to calculate the pausing index for the Ctrl vs KO condition. Here I have given tag directory as input to Homer.Now ...
0
votes
0answers
30 views

Pol_II genome wide occupancy analysis

Paper Figure 1G So in this figure they are analysing the Pol II occupancy in Control,PAF1 KD and LEO1. I have similar data.I would like to know how do I perform this global Pol II occupancy which ...
0
votes
0answers
23 views

homer differential accessibility analysis

I ran homer differential accessibility analysis using this command getDifferentialPeaksReplicates.pl with 7 replicates of Granulocyte monocyte progenitor(GMP) vs Monocyte(Mono) Im bit confused when I ...
1
vote
1answer
142 views

ATAC-seq peak annotation and downstream analysis

I have 7 different cell types, 4 normal cell types and 3 disease cell types. I have done until peak calling. Now I want to do peak annotation. The sample I have is all biological replicates. Should ...
2
votes
2answers
201 views

How do I computationally predict the binding position of a DNA binding protein on the promoters of differentially expressed genes?

I have a list of human genes that have been proven to be up-regulated in a disease condition of interest, using microarray analysis. I also have a protein which according to literature is said to be a ...
0
votes
0answers
515 views

Using HOMER for differential ATACseq analysis

I am trying to understand how I can use HOMER for ATAC-seq paired-end experiments to first find similar peaks between replicates, then compare the combined output files in-between to find ...
4
votes
2answers
553 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 ...
6
votes
1answer
54 views

What's the scaling for HOMER metagenes?

I'm trying to use HOMER to make a metagene profile over gene bodies using a bedgraph file I've generated. The problem is that every time I do, I get really weird scaling on the y-axis. I should be ...