On my RNA-seq data, I ran the HOMER script:
findMotifs.pl /Users/A/Desktop/AA.txt human RNA_sample/ -start -500 -end 500 -len 8,10 -p 4
And I got:
Now, my question is, how can I get ALL the genes included in the identified motifs? For example, how can I get ALL the:
Genes? Importantly, I do NOT want only those that were my input genes, but ALL of the IRF1 motifs.
I have tried a number of things, such as those instructions listed under "Finding Instances of Specific Motifs". None of them work to get all the genes. Presumably, HOMER has access to all the genes in a particular motif. Does anyone know how to access them?
I have to do this to validate the HOMER output with my RNA-seq data.