Supplementary Files

• The human GRCh38 XY reference genome assembly and the comprehensive human v.24 GENCODE annotation used to run the provided examples can be downloaded from the ENCODE consortium portal here:
  https://www.encodeproject.org/data-standards/reference-sequences/

• Circular consensus PacBio Iso-seq data (GM12878 cell line) from Tilgner et al. 2014 can be downloaded in the fastq format from
  http://stanford.edu/~htilgner/2014_PNAS_paper/utahTrio.index.html

• Truth-set small variants for NA12878 from Illumina Platinum Genomes are available in the VCF format at: https://illumina.github.io/PlatinumGenomes/?prefix=2017-1.0/hg38/small_variants/NA12878/

• Report from TranscriptClean run on Tilgner et al. 2014 data that used a short read derived GM12878-specific splice junction annotation and truth-set small variants for NA12878 from Illumina Platinum Genomes for variant-aware correction:
  GM12878_tilgner_v1.0.2_NA12878-snps_report.pdf

• Report from TranscriptClean run on Tilgner et al. 2014 data that used splice junctions derived from the GENCODE v24 annotation and no variant file: GM12878_tilgner_v1.0.2_gencodeSJs_noVars_report.pdf