Fig. 2

The ChimPipe method. a RNA-seq reads are first mapped to the genome and transcriptome using the GEMtools RNA-seq pipeline, and the reads that do not map this way are passed to the GEM RNA-mapper to get reads that split map to different chromosomes or strands. b The split-reads from these two mapping steps are then gathered and passed on to the ChimSplice module which derives consensus junctions associated to their expression calculated as the number of staggered split-reads supporting them. The ChimPE module can then associate each chimeric junction found by ChimSplice to their discordant PE reads, splitting them into the ones consistent and the ones inconsistent with the junction. c The ChimFilter module then applies a series of filters to the chimeric junctions obtained until this point in order to discard false positives, leading to d a set of reliable chimeric junctions to which it associates several pieces of information such as a category (readthrough, intrachromosomal, inverted, interstand, or interchromosomal), and the supporting evidence in terms of number of staggered split-reads and number of consistent PE reads, among others