I am somewhat stupid regarding bioinformatics/ computational stuff in general However I have these lovely ChIPseq data now, that I have started to analyze using Galaxy. Now I want to look for motifs tht are overrepresented in these sequence files, but this seems to be very difficult! And I am not very patient. So I found MEME, which is quite lovely, but I can upload 50 MB only, and every normal fasta file returned from ChIPseq is about 20x as big. So can anyone tell me, either how to use MEME with ChIPseq files (so how to downscale them, or am I using the wrong data set?) or can anyone recommend any other nice algorithm that could be used from a user friendly interface.
I have also tried to get Homer running, but because I only have a laptop and somehow it is very struggle-some to get some server access, I could not run Homer
Thanks a lot for your help,