Thursday 11/14/13

9:30a – 11:45p

Coding / Genomics

  • Fixing fastaread to avoid memory errors
  • Matlab calls char on the list of sequences. If there are short sequences and very long sequences mixed together in the fasta file, this can introduce many gigabytes of blank spaces into the character structure that destroys the RAM cap and causes the computer to freeze.

stain alignment

  • wish I found this function earlier TFLIP = fliptform(T)
  • more project2 progress

Project 2

  • trying in vain to get gene IDs, sequence, and expression level for a unique set of exons.

Cell Culture

  • warming 50 mL flask of new SFX media to room temp.
  • remove media on adhered Kc167 cells, add to media to flask of suspended cells.
  • Add new SFX media to adherent cells.
  • Pellet suspended Kc167 cells by centrifugation, resuspend in new SFX media and transfer to new flask.
  • a few more cells look to be attached in the previously non-adherent cells. Lets hope it continues!


  • Analyze mutation and deletion rate as a function of position
  • Analyze changes in diversity in miSeq data: not substantially more zero hits in one data set or another. Relative diversity of sequences changed substantially.
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