![]() We provide several alternative resources for human fusion transcript detection depending on whether you want to use GRCh37 or GRCh38 reference human genomes and corresponding Gencode annotation sets. TrinityFusion is part of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT), and as such, also leverages the CTAT Genome Library (as also used by STAR-Fusion and FusionInspector. It's easiest to use our Docker or Singularity images to hit the ground running. TrinityFusion does have several software dependencies, however, such as Trinity (see below). Simply unpack the code and it's ready to use (no compilation necessary). TrinityFusion can be downloaded from the TrinityFusion Releases site. Note, TrinityFusion-D is included for the sake of completeness, but TrinityFusion-C and TrinityFusion-UC were found far more impactful and in most cases these alternative modes should be used. ![]() TrinityFusion-UC has been found to be most generally useful for both fusion detection and exploring the assembled unmapped reads for potential transcripts of foreign origin, such as tumor viruses and microbes. TrinityFusion-D uses all input reads for de novo assembly followed by fusion detection. ![]() TrinityFusion-UC uses both the chimeric reads and reads that do not map to the genome as per the STAR aligner for de novo reconstruction followed by fusion detection. TrinityFusion-C uses only chimeric reads identified by the STAR aligner for de novo assembly and subsequent fusion detection. ![]() Note, as of release v0.4.0, CTAT-LR-fusion (which leverages minimap2) replaces the GMAP-fusion module. An overview of the process is illustrated below: TrinityFusion performs de novo transcriptome assembly from RNA-seq data using Trinity, and uses CTAT-LR-fusion to identify candidate fusion transcripts. TrinityFusion leverages chimeric and unmapped reads to assemble fusion transcripts and transcripts of likely foreign origin (microbes and viruses), as a way of facilitating analysis of cancer transcriptomes. TrinityFusion - Fusion and foreign transcript detection via RNA-seq de novo assembly ![]()
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