TARS: Transcript Alignment for RNA Splicing (AUS-418) - #839
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TARS is a new tool for splice-aware RNA alignment. It aligns RNA reads with bwa-mem2 against the genome plus synthetic per-transcript contigs, then lifts the transcript-contig alignments back to genomic coordinates. The output is a normal genomic RNA BAM.
Read
tars/README.mdfor the design, algorithm, and every tunable constant.Gotchas
SpliceFastaBuilderrun. Contig names and spans are keyed together.-rna_unmap_regions) are applied after lift-back on genomic coords, not on the inputchrN_txcoords.-write_liftback_tsvis off by default. Whole-sample the per-record TSVs reach hundreds of GB.-T 19on purpose. Short-anchor supplementaries feed junction rescue, so raising it drops rescues.