Fig. 2

Benchmarking of 38 different StringTie Morex reference-based assemblies. The four plots show different benchmark tests to assess the parameters used in the StringTie assemblies. The graphs do not start from 0 on the y axis. a Transcript number; b the number of HR RT-PCR products that match transcripts; c correlation of the proportions of transcripts in 86 AS events derived from HR RT-PCR and the RNA-seq data using the different assemblies as reference for transcript quantification by Salmon; and d the number of Haruna nijo fl cDNAs that match RTD transcripts. Each plot point represents the result of a StringTie assembly using different parameters (Additional file 1: Table S2). The broken circled plot points at assembly 4, an assembly using STAR defaults (without splice junction filtering) and StringTie defaults. The solid circled plot point at assembly 34 represents the selected optimised StringTie parameters used to produce BaRTv1.0 (see also Materials and Methods; Additional file 2: Figure S3; Additional file 1: Table S2)