Questions tagged [homer]
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14
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How to identify TF binding motifs?
I have DNA sequences from a single gecko species for a set of genes (SULF1, SOX9, SAL1), I wanted to compare the putative promoter sequences for each gene, and compare them to the promoter regions of ...
- 51
1
vote
1
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72
views
What is the required input peak file format for IDR (Irreproducible Discovery Rate)
I have managed to install IDR (https://github.com/nboley/idr) correctly (idr --version returns 2.0.3), but I can't get it to run on my peak files (*.bed) without crashing.
My peak files are generated ...
- 323
1
vote
1
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110
views
How much of the space of motifs have been discovered?
I notice when using tools like HOMER there are two different types of outputs: de novo motifs vs known motifs and it seems no matter what the data is (type of ChIP etc.) there is always a "de ...
- 323
3
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72
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A question on Homer normalization
When using annotatePeaks.pl script from Homer software to create histograms, the output is normalized per bp per peak (on top of normalization to 10 million tags).
What does it mean to normalize per ...
- 279
1
vote
1
answer
356
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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 ...
- 177
1
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0
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21
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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
0
answers
138
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 ...
- 1,774
0
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29
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 ...
- 95
3
votes
1
answer
263
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 ...
- 1,774
0
votes
1
answer
77
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 ...
- 1,774
1
vote
1
answer
423
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 ...
- 1,774
2
votes
2
answers
330
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 ...
- 537
4
votes
2
answers
972
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 ...
- 3,571
6
votes
1
answer
105
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 ...
- 101