Pertea et al. describe a protocol to analyze RNA-seq data using HISAT, StringTie and Ballgown (the ‘new Tuxedo’ package). The protocol can be used for assembly of transcripts, quantification ...

An example is shown for a neighboring pair of S. pombe transcripts (SPAC23C4.14 and SPAC23C4.15, bottom) with substantial overlapping read coverage (gray track), resulting in a contiguous (fused ...