HOMER_command_lines:Using_Sebastians_Output_Data

These line are the general structure I used for the analysis. In previous runs (with Amas Output Data) the setting of -size 200 gave less red star output motifs than the 100.100 setting, so I continued with size 200. When I used -opt with the PWM for the -CACCT(G)- motif the Output file was created but remained empty. The -bg parameter is not usable like we discussed, because it has to be a peak or bed file, therefore a fasta with a scrambled version of our peaks does not work.