Monday 11/18/13

9:00a – 8:30p,

10:00p – 11:45p (remotely)

Assorted Tasks

  • Submitted final BIRS workshop report to BIRS directors
  • Install updates on lab servers Cajal and Tuck and reboot servers.

Ph project

  • launch simulations with matched parameters.
    1. PhM conc variation

Chromatin colors library 3 design


  • Blue has reasonable region fragmentation analysis. Needs more yellow-bounded chromatin regions of different sizes.
  • Short regions didn’t work to well in this library. Hopefully a double index and smaller library will yield better results.
  • All probes should be flipped to the strand of the underlying gene (rather than the whole region being one strand in the direction favored by most of the genes.

Code development for lib3 design

  • IntervalFuseGaps is buggy — I pass it a set of blue regions to fuse and the max region gets shorter.
  • Working on Design of new library with short probes and more overlapping regions.
  • see Lib3Table
  • see new code 11/18/13
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