How to Analyze list of ATAC-seq peaks for specific motifs list?
I have a list of Differentially expressed (DE) genes from RNA-seq and there ATAC-seq peaks. among my DE genes, there are some transcription factors (TF) that are Differentially expressed too (some upregulated and some downregulated). I would like to know if these specific TFs motifs are enriched within my DE genes list, what the best way to approach that problem? I have tried homer but I couldn't find a way to specify the motifs I want it to look for.
many thanks
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eviatar.weizman •
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You can find instance of specific motifs in Homer by providing a motif file. You can run findMotifsGenome.pl with the "-find motif_file.motif" option. Results will be in the form of a tab-delimited text file with each line containing an instance of the motif in the target peaks.