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soedinglab / BaMM_webserver

Webserver for motif discovery with higher-order Bayesian Markov Models (BaMMs)
https://bammmotif.mpibpc.mpg.de
GNU Affero General Public License v3.0
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fix calculation of probabilities in the left flanking region of the model #118

Closed wge11 closed 6 years ago

wge11 commented 6 years ago

The current calculation of probabilities at the left side of the motif sliding window is not accurate. When the position of k-mer is beyond the window of W-length, we should use background probabilities for calculating the probs.

wge11 commented 6 years ago

This is now fixed on the master branch of BaMMmotif2. Additionally, there is a new executable binary called "extractProbs" for extracting probs file (.ihbp/.hbp) from cond. probs file (.ihbcp/.hbcp). It is useful when user use Motif Scan with a BaMM model as input. It can be used for generating properly corrected probs files, which will be used later for plotting the BaMM logo. The command for it is extractProbs <outdir> <.ihbcp file> <.hbcp file> .