WBConfCall 2016.05.19-Agenda and Minutes

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modENCODE tracks for G/Jbrowse

  • A number of users (the latest being Victor Ambros) have observed/complained that features in the modENCODE tracks are not appearing exactly where they should.
  • This is because the tracks are on WBcel215 coords.
  • They need to be remapped to WBcel235 coords. Can hinxton help with this?
  • would that help: Converting_Coordinates_between_releases?


  • upload date: 29th of July?

Pending Help Desk Issues


modENCODE tracks for G/Jbrowse

KH: current coordinates are based on the previous version of assembly. Need to be remapped, a task which has been pending last couple of years. Been deprioritised because it's a massive task.

PWS: Mike Cherry has money to remap. Could he do it? He has new modENCODE DCC.

KH: When it finished first time around, we took responsibility for data. The realignment is a massive job OR remap coord using mapping pipeline. The problem is that Hinxton don’t have data. If they (Hinxton) have data, they could use cluster to remap.

SC: could be done. Doesn’t know where orig GFFs are. Could write script to dump out.

PK: is this the highest value data? We can’t take control of all data for ever. Is this important enough? We could make old data available as legacy. This data is 4 years old, but is it still valuabl?

modENCODE site display: old assembly with old annotation.

SC: makes sense to map forward. Massive project.

PK: Is it sustainable?

PWS : We could ask Mike Cherry. Or we could get some of their money.

Action: Kev to ask Mike (cc PWS) and report back.

If they say no, we do it ourselves.


  • Upload is Friday 1st July
  • Models frozen 3 weeks prior to upload - Friday 10th June

Pending Help Desk Issues

  • We do not go back to WS4!
  • FTP goes back to 100 (and randomly WS77).
  • Action: MAT to respond


  • Progress Report
    • OICR pending. Scott and Sibyl will send draft to PWS by 20th May
    • Hinxton - done
    • Most of CalTech - done
    • MAT to send to PWS by 20th May
    • Deadline is 26th May, but must be in place well before then