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@lucventurini lucventurini released this 07 Mar 17:17
· 747 commits to master since this release
1.0
d039f12

#Version 1.0

Changes in this release:

  • MAJOR: solved a bug which caused a failure of clustering into loci in rare occasions. Through the graph clustering, now Mikado is guaranteed to group monoloci correctly.
  • MAJOR: When looking for fragments, now Mikado will consider transcripts without a strand as being on the opposite strand of neighbouring transcripts. This prevents many monoexonic, non-coding fragments from being retained in the final output.
  • MAJOR: now Mikado serialise also stores the frame information of transcripts. Hits on the opposite strand will be ignored. This requires to regenerate all Mikado databases.
  • MAJOR: Added the final configuration files used for the article.
  • Added three new metrics, "blast_target_coverage", "blast_query_coverage", "blast_identity"
  • Changed the default repertoire of valid AS events to J, j, G, h (removed C and g).
  • Bug fix: now Mikado will consider the cDNA/CDS overlap also for monoexonic transcripts, even when the "simple_overlap_for_monoexonic_loci" flag is set to true.
  • Solved some issues with the Daijin schemas, which prevented correct referencing.
  • Bug fix for finding retained introns - Mikado was not accounting for cases where an exon started within an intron and crossed multiple subsequent junctions.
  • BF: Loci will never purge transcripts
  • After creating the final loci, now Mikado will check for, and remove, any AS event transcript which would cross into the AS event.
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