Questions tagged [homer]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1
vote
1answer
48 views

alternative to HOMER's mergePeaks

Recently, our lab ran a 192 sample experiment through our ATACseq pipeline. In doing so, HOMER's mergePeaks told us that our 512 GB RAM server had too little memory ...
1
vote
0answers
15 views

Nucleotide Frequency - HOMER?

I'm trying to find the frequency of UA dinucleotide in a bed file. I want to convert the bed file to FASTA, count all the UA dinucleotides up, then divide by the total length of the FASTA file. Also, ...
2
votes
0answers
24 views

Finding targets genes of putative transcription factor after homer motif enrichment

Steps I have done I have two cell types to compare one is stem cell and leukemic stem cell Two sets of data for each condition RNA seq and ATAC seq. Did differential expression as well as ...
0
votes
0answers
19 views

How to identify specific motif for chip-seq data

For chip-seq data, I had analyzed the samples until motif discovery using both cluster profiler and Homer for each histone mark. I was wondering what is the efficient method to determine if each GO ...
2
votes
1answer
99 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
1answer
43 views

Pol_II genome wide occupancy analysis

I would like to know how to perform this global Pol II occupancy which is shown here: Paper Figure 1G So in this figure they are analysing the Pol II occupancy in Control,PAF1 KD and LEO1. I have ...
1
vote
1answer
293 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
261 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 ...
4
votes
2answers
719 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
68 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 ...