I have received an excel RNA-seq gene list of differentially expressed genes. I would like to use Homer's Gene based analysis to look upstream of the TSS of these genes and find potential motifs of transcription factors for hypothesis generation, which I can then test in the wet lab.
I've got homer set up and I'm using the command:
findMotifs.pl agmo_id.xlsx mouse RNA_seq/ -start -400 -end 100 -len 8,10 -p 4
However, homer spits back that it is unable to open the file. I tried saving it as a tab-delimited plain text file, but I have the same response.
The file contains the accession numbers and the log2 fold change of the genes. The accession numbers are ensembl.
What file format should I be saving it as? I've tried tab delimited, comma delimited and basic excel files, but none seem to work.