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Versions

0.90.5

  • hg19 TXdb included
  • improved bed2fa script, now TXdbgen runs faster.
  • option for trunk size when mapping (-t)
  • option –force-no-qsub
  • now keeps bowtie mapping results
  • deleted some IR events with intron_size=0, updated all TXdbs, please reinstall SpliceTrap to download the new databases

0.90.1 (Nov 1, 2011)

  • fixed a bug in bed2FA (id:chr)
  • fixed a bug in SpliceChange (id:sort)

0.90 (Sep 29, 2011)

  • SpliceChange included now.
  • TXdbgen now outputs evidences for each event, databases updated accordingly.
  • noirm options added for SpliceTrap/PostAnalysis/SpliceChange.
  • fixed a bug for bowtie mulitiple threads.

0.88 (Sep 10, 2011)

  • Bug fixed for qsub.
  • gtf file supported by TXdbgen.
  • Bowtie multiple threads supported now.

0.87 (Jul 7, 2011)

  • Optimized for Galaxy.
  • fixed bugs for Ubuntu.
  • Post analysis steps optimized.
  • Supporting single-end reads.
  • Database updated.

0.86 (May 16, 2011)

  • Starting from this version, TXdb generator is provided.

0.85 (Apr 16, 2011)

  • TXdb updated, with newer version of RefGene and Unigene.
  • New IDs assigned in TXdb.
  • Fixed a minor bug[id:j13].
  • Fixed a minor bug[id:clean tmp files]
  • TXdb updated, dbCASE now has knowngene as evidences.
  • TXdb updated, with more species, including mm9 and rn4.
  • ./db structure changed.
  • Directory struture changed.
  • Installation optimized[id:Noini].

0.82c (Nov 12, 2010)

  • Estmation step written in C++.
  • Optimization at the cutoff step.
  • fixed a bug for Ubuntu.
  • If Qsub is not supported, use local cpu.
  • Utilized on Galaxy in CSHL, Thanks, Gordon and Hannon lab!
  • Optimization on output format.
  • R script update.

0.82

  • Splitting into chrmosomes to make estimation faster.
  • Supporting bowtie and RMAP, no longer support ELAND.
  • Optimization on IO.