Question: Identifying the orientation of a CTCF motif?
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gravatar for Sinji
5 weeks ago by
Sinji2.5k
UT Southwestern Medical Center
Sinji2.5k wrote:

I'm analyzing some CTCF ChIP-seq data, i'm interested in recording the orientation of CTCF sites as they have been shown to have important roles in the underlying biology. I can't seem to find any information on how to do this, despite it being fairly popular. Perhaps just not using the right search terms. Any ideas?

ctcf chip-seq • 185 views
ADD COMMENTlink modified 5 weeks ago by simon.vanheeringen110 • written 5 weeks ago by Sinji2.5k
1
gravatar for simon.vanheeringen
5 weeks ago by
simon.vanheeringen110 wrote:

Use the CTCF motif to scan the peaks. The directionality of the motif match presumably tells you the CTCF orientation.

For instance, you can use this CTCF motif (save in a tab-separated text file):

>C2H2_ZF_Average_200
0.081779124449  0.816566257007  0.0503624700168 0.0512921485275
0.00454091560919        0.992667683465  0.000844143310774       0.00194725761473
0.729859139975  0.0190570790231 0.169685871266  0.0813979097358
0.03204130191   0.630845335167  0.323279272143  0.0138340907799
0.123093260475  0.494372096106  0.0637025611488 0.31883208227
0.901255804964  0.0197757515554 0.0514199924903 0.02754845099
0.0032323521056 0.00108383141845        0.992842879801  0.00284093667487
0.416975026239  0.006048776898  0.5707589234    0.00621727346346
0.0353963142494 0.0316137184991 0.579714716892  0.353275250359
0.00986220321585        0.00125463577494        0.985814739139  0.00306842187041
0.0950088577041 0.0355503655191 0.815560120364  0.053880656413
0.0980555406351 0.793094920278  0.0235874699945 0.0852620690928
0.362317695845  0.0268864366115 0.577387352297  0.0334085152465

For scanning, you can try GimmeMotifs. Using gimme scan you can use this motif to scan your peaks. Replace hg38 with your genome of interest.

$ gimme scan CTCF_peaks.bed -p CTCF.pwm -g hg38 -b > CTCF_motifs.bed

This will report at most one match per peak, with an estimated FPR of 1% based on random genomic sequences. The strand column in the BED output will tell you the direction of the motif.

ADD COMMENTlink written 5 weeks ago by simon.vanheeringen110

This is excellent, thank you very much!

ADD REPLYlink written 5 weeks ago by Sinji2.5k
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