**DerTALE** filters predictions of TALE target boxes by the presence of differentially expressed regions in a defined vicinity around a predicted target box.

As input, *DerTALE* requires a list of target box predictions as generated by the *Predict and Intersect Targets* tool of AnnoTALE or by the *PrediTALE* tool. Besides, DerTALE also accepts prediction outputs of other tools like TALE-NT or Talvez.

For determining differentially expressed regions, *DerTALE* also needs mapped RNA-seq data after *Xanthomonas* infection (treatment) and control in BAM format, which is the standard output format of most mappers, and may be generated from the SAM format using samtools. For each BAM file, *DerTALE* also needs an index file with the same base name as the BAM file but additional extension ``.ba`` (as generated by samtools).

Further parameters that can be specified include the number of predictions in the list that are considered (counting from top), the width of the region in which differential expression is considered, the width of the window that needs to be differentially expressed, a pseudo count on the count profile, the measure for comparing replicated, and a threshold on the log (base 2) differential abundance (e.g., ``1`` for a two-fold induction).

If you experience problems using *DerTALE*, please contact_ us.

.. _contact: mailto:grau@informatik.uni-halle.de