Script of the article of LEMAIRE et al (2019)

This respository contains the scripts used to produce the analyses in the article of LEMAIRE et al entitled :

Splicing factors and chromatin organization enhance exon recognition by alleviating constraints generated by gene nucleotide composition bias

It contains many subdirectories. Each subdirectory contains a doc folder that contains a detailled description of the scripts in src folder.

Here is a short description of what every subdirectories contains:

• Database_creator : the scripts under its src directory, allow to create two sqlite3 databases fasterDB_lite.db and sed.db. Those databases are used by the scripts in Clip_analysis, Figure_ESA, Figures_SL and GC_rich_AT_rich_exon_list.
• Figure_ESA : the scripts under its src directory, allow to create the heatmaps and the correlation figures in the article.
• Figures_SL : the scripts under its src directory allow you to create some suplementary figures of the article (i.e the figures representing a lot of boxplots : one boxplot for each splicing factor)
• Clip_analysis : the scripts under its src directory allow you to create the clip density figures.
• GC_rich_AT_rich_exon_list : the scripts under its src directory allow to create the boxplots, barplots and violin plots of many differents features (minimum free energy, number of branch points, number of UNA and T-rich low complexity sequences) for the AT- GC- U1- and U2-exons groups. (see the method in the article for more precision)