Custom code used for the analysis in Ghavi-Helm et al., 2019

Custom code used for the computational analyses in Ghavi-Helm*, Jankowski*, Meiers* et al. paper "Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression". The project involved whole genome sequencing, mate-pair, RNA-seq, Hi-C and Capture-C data from highly rearranged balancer chromosomes in Drosophila melanogaster.

The software is provided "as is", in the hope that it will be useful, but without warranty of any kind. For historical reasons, the code is organized into following subdirectories:

• drosophila_balancer – authored by Sascha Meiers, involving SNV and SV calling from whole-genome and mate pair sequencing data, as well as RNA-seq analysis
• Capture-C – authored by Aleksander Jankowski, involving Capture-C data analysis
• Hi-C – authored by Aleksander Jankowski, involving Hi-C data analysis, as well as Hi-C, Capture-C and other data plotting
• Hi-C-ggbio – authored by Sascha Meiers and Aleksander Jankowski, for plots combining Hi-C contact maps, gene expression and gene models using ggbio package.

The contents of these subdirectories were accordingly located in:

• /g/korbel/shared/projects/drosophila_balancer
• /g/furlong/project/37_Capture-C
• /g/furlong/project/33_Hi-C
• /g/furlong/project/33_Hi-C/Hi-C-ggbio.

Software dependencies are listed in the Life Sciences Reporting Summary linked to the article.

In case of any questions, please contact Aleksander Jankowski <aleksander.jankowski(at)embl.de>.