Questions tagged [homer]

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2
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2answers
158 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
418 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
397 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
50 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 ...