recentering peaks on the center of motif

Question

[mary99]

Hello everybody,

In my chip-seq data I retrieved all motifs that are located under peaks.Then I want to recenter my peaks based on the middle point of motifs.my question is that what is the best cut sites of this new peaks?I means to which distance I should extend the middle of motifs in both sides in order to reach a good peaks?theses peaks then should be used to measure the distance from TSS?

p.s.peaks are for a transcription factor

Thanks in advance

[rioualen]

I don't get it, why not just measure the distance between motifs and TSS?
I'm not sure peaks should be shifted, sometimes motifs are not in the center but this information has its importance too. You can even find dyads motifs under peaks, that are located one the sides of the peak.

Answer 1

[Sukhi Singh]

I would say you can run several tests, finding neighbouring genes with no extension at all, one with 50 bp and 200bp extension.

Find out what are you losing in terms of genes and then decide for yourself.

Also, check this out Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal With The Merged Peaks (Peak Consensus) ?