I’m analyzing ChIP-seq data and currently performing a de novo motif analysis using MEME. The output shows a high number of repeat motifs (e.g. GAGAGAGAGAGA) and only as the 10th motif I find the motif of the TF I chipped. The data is very repeat rich, but repeat masking also results in loss of my TF motif as it is within these repeats. I’m afraid that this will not enable me to identify any other co-occurring motifs of interest, so I was wondering if there is a better approach.
Is there a way to tell MEME not to recognize these simple repeats as motifs? I’ve not found out how to do this just yet.
Do you recommend another tool which is more suitable for repeat-rich sequences?
Thank you very much!