Hi everyone,
i have used meme to do some analysis on some sequences and got the output. The next step is to use tomtom to compare the result, i have a database of motifs hundreds files looks like something like this:
Pos A C G T
1 0.150033322225925 0.716511162945685 0.0750583138953682 0.0583972009330223
2 0.0255348955680081 0.0127992868059093 0.948866530820173 0.0127992868059093
3 0.0189260563380282 0.874056841046278 0.106954225352113 6.2877263581488905
4 0.0189260563380282 0.97466046277666 0.00635060362173038 6.28772635814889e-05
How can i make use of these files to compare the output from meme use command line version meme? i know i have to convert the format of these motifs files, i think i have tried all the methods shown in this link http://meme-suite.org/doc/motif_conversion.html, but none of them work . Any help will be appreciated. many thanks
The methods do not work because your matrix is not in a standard format. i suggest you, to convert in beeml format. Basically, and put an # at the beginning of the line with a generic name and substitute the 1,2,3,4 at the beginning of the lines with A,C,G,T of and then run again beeml2meme.
Hi Girolamo, thank you very much for your response, i somehow changed the format of my files into something like this in R,
# M0004_1.02
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A 15 3 2 2 0 6 16 49
C 72 1 87 97 1 63 77 7
G 8 95 11 1 99 14 1 30
T 6 1 0 0 0 18 6 14
# M0004_1.02
A 15 3 2 2 0 6 16 49
C 72 1 87 97 1 63 77 7
G 8 95 11 1 99 14 1 30
T 6 1 0 0 0 18 6 14
however beel2meme does not work on both cases, do you know what the problem would be? many thanks
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