scripts_and_data_TE_paper

These are all the protcolos used and results produced for the paper "Regulation of transposable elements: interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster" by Ana Marija Jaksic, Robert Kofler and Christian Schlötterer. I did not include some intermediate files (for example intermediate fasta files or pileups) due to space reasons but they can be generated with the provided code. In file "hello.txt" you will find a shortcut to most important data and scripts. AM :)