Tag: findMotifsGenome.pl

Abstract While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2–27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal…

Models for single-cell ATAC-seq data In single-cell ATAC-seq data, \(x_{ij}\) is the number of unique reads mapping to peak or region j in cell i. Although \(x_{ij}\) can take non-negative integer values, it is common to “binarize” the accessibility data (e.g., [19, 74, 133,134,135]), meaning that \(x_{ij} = 1\) when…

homer motif search 0 I have used findMotifsGenome.pl from HOMER to find motif, its output have many files including knownResults.html and homerResults.html. which output file should I consider for my downstream studies and what is difference between these two files? search motif HOMER • 23 views Login before adding your…

Assign gene to peak in bulk ATAC-seq 0 Hi all, I have some questions about bulk ATAC-seq that I don’t understand, hope that you can help. If we have a task to identify which genes in a sample (such as diseased) are in open chromatin region, is that using differential…

Help with an error with Homer 0 Hi all, I looked for this error but still don’t know why. Would you please have a suggestion? Thank you so much! findMotifsGenome.pl homer_format hg38 MotifOutput/ -size 200 -mask -len 8 -preparsedDir preparsed_dir I got these files in the output folder: hg38r.200.cgbins hg38r.200.cgfreq…

Help to get differential_peaks.bed to use for findMotifsGenome.pl? 0 Hi all, I am trying to use the command findMotifsGenome.pl from HOMER that needs differential_peaks.bed file as input. I used nf-core/atac-seq then DiffBind but not sure how to get differential_peaks.bed file. Would you please have a suggestion? Do I need to…

Hi All, I did and ATAC-Seq experiment in different cell lines and I was curious to see if they have different motifs in the open chromatin. I was planning to use HOMER for this, but running from linux bash: findMotifsGenome.pl ATAC_d001_peaks_called_with_homer.txt hg38 ATACAd001_FIND_MOTIF I got this message of error (see…

Identify binding motifs within large super enhancer region 1 Hello, From my H3K27ac ChIP seq data, I have identified 500 super enhancer regions using Homer’s findPeaks -style super. From the super enhancer regions, I found 4 enriched binding motifs within the 500 super enhancer regions using Homer’s findMotifsGenome.pl. First, I…

How to find peaks with specific TFs identified by HOMER 1 Hi, I have attempted to utilize HOMER to identify peaks associated with specific transcription factors (TFs). I employed “findMotifsGenome.pl” and “annotatePeaks.pl” to extract sequences linked to these TFs. In theory, the results obtained from both methods should be identical….

Can I use the summits.bed from MACS2 on HOMER 1 I understand that to run HOMER you need BED files, so could I use the BED output file from “macs2 callpeak” to run “findMotifsGenome.pl”? Homer Macs callpeak bed • 40 views • link updated 2 hours ago by seidel 8.3k…

Problem with HOMER -find <motif file> 0 I am trying to search for specific motifs in my set of promoters. It should be possible with the option -find *.motif I know that there are for sure some occurrences because I have found them with search function in Notepad. However HOMER…