TAFLab/GenERA_GitHub: GenERA pipeline

Scripts used to conduct the bioinformatics in the "In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPRCas9 genome engineering" manuscript.

The GenERA pipeline aims to understand the impact of genomic deletions on transcript abundance. To do so the gDNA and cDNA from edited cells are subjected to targeted NGS (see Method section), meaning that the same amplicon (genomic sequence encompassing the edited region) is analyzed in both gDNA and cDNA. The GenERA pipeline takes as input the pair-end reads, stored as .SAM files, from the gDNA and cDNA library. Editing by CRISPR:Cas9 causes genomic deletions, which vary in size and coverage across the amplicon. The aim of the pipeline is to extract from the sequencing reads all deletions, sort them by unique deletion patterns (UDP), and match them between gDNA and cDNA libraries. By comparing the read count ratio between cDNA and gDNA libraries for a given unique deletion pattern (UDP) to the similar ratio for the non-edited amplicon, it is possible to assess the effect of each genomic ablation on transcript level.