Hi everyone. I'm trying to find the motifs bound by my ChIP-ed protein using Homer. I don't have knowledge regarding NGS analysis. The analysis was done by my labmate who understand programming languages but lack of experience in analysing ChIP-seq.
When going through the result list, I found that there are 2 obvious issues happened.
1) The % of target vs % of Background sequences with Motif are very close throughout the list. When this happened, does it mean that the motifs found are actually not/ very lowly enriched in my ChIP-ed sample?
2) The "SeqBias: CG bias" appears as the 1st ranked motif in my list. I know this indicates that the analysis parameter is not appropriate as stated in http://homer.ucsd.edu/homer/motif/practicalTips.html. This is probably related to the normalization to either by total GC-content or CpG-content if I understand the tutorial correctly. Should I just adding "-gc" to the motif finding command to solve this problem? If having this problem on my list, do other results on the list still valid?
Thanks very much!