Motif finding ChIPseq - (Nov/18/2013 )

Dear all,

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,

Claudia

Hi Claudia,

I agree that MEME is the right tool to do de novo motif search in your chip-seq data. 

I think you need to find some bioinformatics people to help with your data analysis. Such high throughput data is not something that can be handled without using special programs. For example, for MEME analysis, you may need to install the program in a linux/unix box, and run the program using command prompt. Online programs usually have limits on the amount of data you can upload. 

Hi Epi,

thanks a lot for your reply. It's great to hear that it might be possible to process ChIPseq files with MEME from the command line. I'll try it (with expert's help :))