Opened 4 weeks ago

Last modified 3 weeks ago

#1025 assigned enhancement

Release exporter should support StringTie data

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Reggie v4.16
Component: net.sf.basedb.reggie Keywords:


The current implementation of the release exporter only supports Cufflinks data. There are several things that need to be diffent when exporting StringTie data.

  • The array design is different. No features have been imported to the database so the exporter may have to parse the GTF file (unless we simply can copy it as it is)
  • A different list of data files (files to export must be white-listed)
  • Expression data is not in a FPKM file. If we want to export an expression matrix, we need to get this from other files.

Change History (2)

comment:1 Changed 3 weeks ago by nicklas

  • Status changed from new to assigned

comment:2 Changed 3 weeks ago by nicklas

(In [4689]) References #1025: Release exporter should support StringTie? data

Fixed so that the exporter doesn't crash when trying to export StringTie data. Array design files and expression matrix files are created but empty. JSON files are created with "gene.tsv" and "transcript.gtf" white-listed for exporting.

This is only a temporary solution that needs more work before it can be used in production.

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