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find_CTCF_motifs_strategy.txt
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find_CTCF_motifs_strategy.txt
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### KREBS PLOT ###
MEME version 4
ALPHABET= ACGT
strands: + -
Background letter frequencies
A 0.25 C 0.25 G 0.25 T 0.25
MOTIF MA0139.1-CTCF-CpG5
letter-probability matrix: alength= 4 w= 19 nsites= 913 E= 0
0.095290 0.318729 0.083242 0.502738
0.182913 0.158817 0.453450 0.204819
0.307777 0.053669 0.491785 0.146769
0.061336 0.876232 0.023001 0.039430
0 1 0 0
0 0 1 0
0.043812 0.578313 0.365827 0.012048
0.117325 0.474781 0.052632 0.355263
0.933114 0.012061 0.035088 0.019737
0.005488 0.000000 0.991218 0.003293
0.365532 0.003293 0.621295 0.009879
0.059276 0.013172 0.553238 0.374314
0.013187 0.000000 0.978022 0.008791
0.061538 0.008791 0.851648 0.078022
0.114411 0.806381 0.005501 0.073707
0.409241 0.014301 0.557756 0.018702
0.090308 0.530837 0.338106 0.040749
0.128855 0.354626 0.080396 0.436123
0.442731 0.199339 0.292952 0.064978
URL http://jaspar.genereg.net/matrix/MA0139.1no
MOTIF MA0139.1-CTCF-CpG7
letter-probability matrix: alength= 4 w= 19 nsites= 913 E= 0
0.095290 0.318729 0.083242 0.502738
0.182913 0.158817 0.453450 0.204819
0.307777 0.053669 0.491785 0.146769
0.061336 0.876232 0.023001 0.039430
0.008762 0.989047 0.000000 0.002191
0.814896 0.014239 0.071194 0.099671
0 1 0 0
0 0 1 0
0.933114 0.012061 0.035088 0.019737
0.005488 0.000000 0.991218 0.003293
0.365532 0.003293 0.621295 0.009879
0.059276 0.013172 0.553238 0.374314
0.013187 0.000000 0.978022 0.008791
0.061538 0.008791 0.851648 0.078022
0.114411 0.806381 0.005501 0.073707
0.409241 0.014301 0.557756 0.018702
0.090308 0.530837 0.338106 0.040749
0.128855 0.354626 0.080396 0.436123
0.442731 0.199339 0.292952 0.064978
URL http://jaspar.genereg.net/matrix/MA0139.1no2
MOTIF MA0139.1-CTCF-CpG15
letter-probability matrix: alength= 4 w= 19 nsites= 913 E= 0
0.095290 0.318729 0.083242 0.502738
0.182913 0.158817 0.453450 0.204819
0.307777 0.053669 0.491785 0.146769
0.061336 0.876232 0.023001 0.039430
0.008762 0.989047 0.000000 0.002191
0.814896 0.014239 0.071194 0.099671
0.043812 0.578313 0.365827 0.012048
0.117325 0.474781 0.052632 0.355263
0.933114 0.012061 0.035088 0.019737
0.005488 0.000000 0.991218 0.003293
0.365532 0.003293 0.621295 0.009879
0.059276 0.013172 0.553238 0.374314
0.013187 0.000000 0.978022 0.008791
0.061538 0.008791 0.851648 0.078022
0 1 0 0
0 0 1 0
0.090308 0.530837 0.338106 0.040749
0.128855 0.354626 0.080396 0.436123
0.442731 0.199339 0.292952 0.064978
URL http://jaspar.genereg.net/matrix/MA0139.1no3
Manual inspection of the FIMO output showed that this actually worked very well.
There is a few problem:
1. what to do about peaks that have more than one motif? : combine them!
No more problems :)