Identify motifs in long enhancer regions

[Mikaela Dea Kunika]

Hello,

I am working with H3K27ac ChIP seq data. I have identified long enhancer regions (around 50-90kb) and would like to identify the transcription factor binding motifs that bind within one of these regions.

So far, I have used MEME for motif discovery, but the motifs that are output are mostly repeat simple sequences. I have already masked my sequences using RepeatMasker and dust. For additional context, I specify anr for motif distribution and motif width ranges from 6-20bp.

How can I filter out the simple sequences that are being detected as motifs in MEME? Is there a better suited tool in MEME Suite? 

Thank you!

[cegrant]

Hi mkunika,

Did you have RepeatMaser and dust mask out by setting bases to lower case or by setting them to 'N' or 'X'? If you set them to lower case that won't work, MEME will just convert them to upper case again. Make sure they are set to 'N' or 'X'.

Charles

[Mikaela Dea Kunika]

Hi Charles,

I have RepeatMasker set to masking the bases with capital N.

Are there any other alternatives to filter out simple sequences in motif discovery with MEME?

Thank you!

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[cegrant]

Hi mkunika,

You might also look at Tandem Repeat Finder. I used it for the analysis I did for the MCAST paper. One of the intermediate/advanced options is Maximum Period size, which I found had to be set to several thousand.

Charles