Automated denovo motif analysis
Dear all, I have a question-
I have thousands(2-3 thousand ) bed files, for which I would like to derive denovo motifs.
Which package would you suggest such that it is done the fastest? I am more interested in percentile frequencies rather than graphical output.
best
Abhi
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ddiez
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swttalyan •
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swttalyan •
1 answer
Personally, I would probably use the meme program in the MEME suite for motif discovery and analyze the results in R. If you want to keep the whole analysis in R a possibility is the rGADEM Bioconductor package for motif discovery. Take a look also to the package MotIV for further motif analyses.
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