Publicly available Illumina RNA-seq data sets of D. melanogaster [SRA:SRR166809] and a human melanoma sample [SRA:SRR018261-62] were downloaded from the National Center for Biotechnology Information short read archive. The 454 sequencing data for a human umbilical vein RNA-seq experiment [27 (link)] and RNA capture sequencing experiments of human fibroblasts [24 (link)] were retrieved from the Gene Expression Omnibus under [GEO:GSM951482] and [GEO:GSE29040]. The RNA-seq sample for HEK293 cells investigated in [5 (link)] was retrieved under [GEO:GSE43574]. Finally, we applied our algorithm to a C. elegans data set [SRA:SRX151602] to investigate RNA leader trans-splicing. All of these data sets are non-strand specific. In addition, we analyzed a strand-specific prostate cancer data set (see Additional file 1 ).
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