bioRxiv v2

• set --max-intronlength-ends to 500kb, this is due to cases
  where GMAP soft-clips the terminal exon(s) if they are over
  10kb (default value)
• set chimeric alignment option to match min clip length
• consider partial novel junctions when checking for presence of
  novel intron (may also be novel exon). This may occur in cases
  of overlapping exons that can obscure novel exons.

bioRxiv v1

Release corresponding to v1 pre-print submission to bioRxiv: https://doi.org/10.1101/2020.06.03.131532