Computational Regulatory Genomics

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Cseq-Simulator (Crosslinked-sequence Simulator)

Cseq-Simulator is a pipeline for realistic RNA-Clip simulations. It mimics key steps of Clip protocols and allows with user provided profiles to simulate any diagnostic event distribution (RBPs). Furthermore, Cseq-Simulator is very individual and lets the user provide a list of RBP binding sites or transcipt abundance profiles.

FIMO as part of MEME

See the Cseq-Simulator publication for more information.

Cseq-Simulator source code can be downloaded here:
Cseq-Simulator v1.02 (Documentation)
Cseq-Simulator v1.01  (Documentation)
Cseq-Simulator v1.00  (Documentation)

Patch notes:

  • fixed small buggs
  • added options to select a combination of diagnostic events to be introduced (each diagnostic event has an option for a profile)
  • added option to provide a profile for read length distribution (for iClip)(option -tl, however, not yet in documentation)
  • added the possibility to provide a tuple instead of an INT for read length that comprises lower and upper boundaries (for iClip; -x T must be set)
  • added a global binding site affinity
  • added option to increase memory usage


  • now supports compressed transcriptome files (tar.gz)
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