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Added -y option in the README
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Florian Schmidt committed Jan 26, 2017
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Expand Up @@ -47,6 +47,7 @@ The optional parameters are:
* -n Indicates that the file in -b contains the average signal in the peaks in the specified column. In this case the -d option is not required to obtain scaled TF affinities.
* -c Number of cores used within TRAP.
* -f A gtf file containing genes of interest. Only regions contained in the file specified by the -b option that are within the window specified by the -w option around these genes will be annotated.
* -y Flag indicating whether the entire gene body should be annotated with TF affinities. A window of half the size of the -w option will be additionaly considered upstream of the genes TSS.

Depending on the used arguments, TEPIC produces files containing:

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