RNA-seq revisions of C. briggsae gene models. (A) An intron is confirmed if the predicted intron in the hybrid gene model is supported by an RNA-seq-defined Illumina intron. (B) An intron is replaced by an RNA-seq-defined Illumina intron if the predicted intron overlaps with the Illumina intron but is not identical to the Illumina intron. (C) A new intron is created if an Illumina intron overlaps with a coding region. (D) A predicted intron is removed if it overlaps with an Illumina exon and it is not supported by any Illumina intron and it does not overlap with any Illumina intron. (E) A 3′ intron is created if an Illumina intron overlaps with the 3′ most exon. A new 3′ exon is also created that contains a stop codon. (F) A 5′ intron is created when an Illumina intron overlaps with the 5′ most exon. A new 5′ exon is also created that contains a start codon.
