How to Analyze list of ATAC-seq peaks for specific motifs list?

Question

[eviatar.weizman]

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

[patelk26]

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.

findMotifsGenome.pl peakfile hg18 MotifOutputDirectory/ -find motif1.motif > outputfile.txt