This is the Linux app named PTESFinder whose latest release can be downloaded as ptesfinder_v1.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions and canonically spliced transcripts. This approach increases the confidence in PTES supporting reads. Reads emanating from template-switching events are often characterised by large indels when aligned to the transcriptome. PTESFinder uses additional filters to exclude reads with ambiguous alignments around PTES exon-exon junctions, further increasing confidence in these supporting reads. PTESFinder identifies more PTES structures than other published methods whilst maintaining high specificity.
Unix Shell, Java
This is an application that can also be fetched from https://sourceforge.net/projects/ptesfinder-v1/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.