Hi everyone,
I am using findMotifs from Homer to find enriched motifs in a set of genes of interest. This is the first time I am doing this and I'm a bit confused with some of the results.
I am getting a lot of entries with SeqBias, with combinations of different nucleotides. I was checking the practical tips of HOMER (http://homer.ucsd.edu/homer/motif/practicalTips.html) and regarding this Low-complexity entries, they say the following:
"These motifs typically arise when a systematic bias exists between target and background sequence sets. Commonly they will be very high in GC-content, in which case you may want to try adding "-gc" to your motif finding command to normalize by total GC-content instead of CpG-content.
Other times this will come up when analyzing sequences for various genomic features that have not been controlled for in the background - for example, comparing sequences from promoters to random genomic background sequences in some organisms will show preferences for purines or pyrimidines. HOMER is very sensitive, so if there is a bias in the composition of the sequences, HOMER will likely pick it up. Autonormalization in the new version minimizes this problem."
This information seems to me, does not apply to my case, since I am using background random sequences created from my target sequences. However, I am not fully sure.
Should I re-run the analysis, correcting for the total GC-content? Or should I keep as is?
Thanks in advance.
