I my ChIP-seq data, I used HOMER to call motifs. Now I have few regions of interest and I want to look at the DNA sequence which motifs are present. Any suggestion of tools how can I do this?
I attached the following example from M. R. Mansour et al., Science (80). 346 (2014) to show what I want to generate. Thanks!
You could visualize the regions of interest in IGV or UCSC Genome Browser
If you use the UCSC browser you can enable the Public Trackhub 'JASPAR 2018 TFBS', which is good for the following genomes: hg19, hg38, ce10, dm6, sacCer3, and araTha1.
You can enter the coordinates of your sites of interest as Custom Tracks, as BED formated genome coordinates.
I found this tool (CIS-BP) that helps to do the job. Thanks all for your valuable suggestions.
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FIMO from MEME suite is an option. Load in your regions and filter for the motifs that popped up in Homer.