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Hi all,
I'll cut right to the chase...I want to identify regions within a chip seq data set that contain a potential co-factor motif. There seems to be lots of programs to indentify motifs within sequences but they don't tell you in which peak sites they occur.
I want to isolate the peaks occupied by my chip TF and the potential co-factor only so that I can look and see if genes specifically associated with those peaks show similar expression ie. they're potentially co-regulated.
I originally used the seqpos motif tool in cistrome to look for potential overrepresented motifs in chip seq data to look for potential co-factors. I then tried using 'Screen all motifs' - 'Given a motif, find all regions that match the motif ' but I can't get it to work. I keep getting an error, does anyone know of another program that can do this?
Many thanks
Livi
I'll cut right to the chase...I want to identify regions within a chip seq data set that contain a potential co-factor motif. There seems to be lots of programs to indentify motifs within sequences but they don't tell you in which peak sites they occur.
I want to isolate the peaks occupied by my chip TF and the potential co-factor only so that I can look and see if genes specifically associated with those peaks show similar expression ie. they're potentially co-regulated.
I originally used the seqpos motif tool in cistrome to look for potential overrepresented motifs in chip seq data to look for potential co-factors. I then tried using 'Screen all motifs' - 'Given a motif, find all regions that match the motif ' but I can't get it to work. I keep getting an error, does anyone know of another program that can do this?
Many thanks
Livi
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