Hi!
I have done a chip-seq experiment and obtained a number of peaks. Using MACS v1.4 I obtained 1262 peaks with IDR < 0.01 between my two samples. Since my samples contain a lot of PCR duplicates and the MACS algorithm supposedly contains a lot of false positives I would like to validate my peaks by searching for the known sequence to which the TF should bind.
The tool Centrimo (http://meme.nbcr.net/meme/doc/centrimo.html) in the MEME suite of tools seems to be the right tool for the job however I am having issues with getting the known sequence in the right format.
The known sequence is the E-box (5'-CANNTG-'3). I have searched transfac and JAPSAR but can't seem to find anything that even remotely resembles anything that I could use as input to either Cetrimo or any of the MEME conversion tools.
Could anyone please guide me in the right direction of finding the TRANSFAC motif of the E-box motif or how to convert this sequence into the minimal MEME format?
Your help is very much appreciated.
I have done a chip-seq experiment and obtained a number of peaks. Using MACS v1.4 I obtained 1262 peaks with IDR < 0.01 between my two samples. Since my samples contain a lot of PCR duplicates and the MACS algorithm supposedly contains a lot of false positives I would like to validate my peaks by searching for the known sequence to which the TF should bind.
The tool Centrimo (http://meme.nbcr.net/meme/doc/centrimo.html) in the MEME suite of tools seems to be the right tool for the job however I am having issues with getting the known sequence in the right format.
The known sequence is the E-box (5'-CANNTG-'3). I have searched transfac and JAPSAR but can't seem to find anything that even remotely resembles anything that I could use as input to either Cetrimo or any of the MEME conversion tools.
Could anyone please guide me in the right direction of finding the TRANSFAC motif of the E-box motif or how to convert this sequence into the minimal MEME format?
Your help is very much appreciated.