I have transcription factor chip seq bed files data for multiple transcription factors.
I'd like to extract TF motifs positions for every read, so i first narrowed the chip seq peaks to include only 30 bases around the peak center.
Ideally I need to extract the exact positions of the TF binding, so I thought I could use MEMEchip for identifying the motifs but I didn't get a motif or positions.
My question is first what algorithmprogram should I use and how, and if it's indeed MEMEchip, what parameters I should use and how.
Thank you for your help!