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4.1 years ago
may6343
•
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Hello everyone, 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 algorithm\program should I use and how, and if it's indeed MEMEchip, what parameters I should use and how. Thank you for your help!
The task before you greatly depends on data quality you have and how well conserved the motifs you are after are.
It is my understanding that for meme-chip, you provide the whole peaks, not only some cut-out region. If you are confident about the motif position, then do the cut-out and use meme directly (instead of meme-chip).
I've used both tools, I didn't use bed files directly (I've always extracted the sequences to fasta format prior to analysis) so I can't give you any insight on that, but I've ended up using only meme and not the meme-chip. If your TF happens to bind to 2 motifs at once with variable spacer, use tool dedicated for that (e.g. bioprospector or something more recent).