Wednesday 11/20/13

10:15a – 10:00p


  • prepare slides for chat with Levine
  • Reply to SW

Genome Analysis

Mi Seq analysis of off target hybridization sequence bias

  • New strategy:
    • Generate new fasta file with the entry ID number as the first 5 digits (00000 – 99999).
    • num2str this and use that to pull out the sequence entry from the loaded fasta file.
    • now we have the reference sequence and the read sequence without any massive strfind calls.

mRNA read alignments

  • installed FCIV (microsoft’s checksum tool).
  • ran on rep1 BAM data
  • Attempted running cufflinks on Tubigen Galaxy browser following successful upload of BAM file.
  • Tubigen Galaxy gives error cufflinks not found ?
  • Did not have genome specified or reference gtf file uploaded. Uploading now.
  • All modules in RC example are many versions out of date.
  • RC computing is

Planning next round of probe sequencing

  • 8 sublibraries, 2x PCR -> prep for sequencing with single round PCR addition of adapters
  • prep each of 8 sublibraries to make probes, T7 reaction, RT reaction (with cy3 primer)?, oligo-cleanup
  • prep the probes for sequencing with single round PCR adapter additions

Cell culture

  • passage cells.
  • both new flasks look good. Density substantially higher on original flask, let’s split this one again tomorrow.

Ph modeling

  • running diff-binding model for PhM conc effects (instead of capping model)


  • Making slides for chat with ML
  • started presentation on GoogleDocs using the last update for Ting Wu and the SDB slides as a stub.
  • working on getting more clearly contrasted images of chromatin domains for slides

STORM analysis

  • analyzed AbdA (twice, overwrote data with D11)
  • analyzed D11 data

STORM to image / re-image

  • E10rna (focus lost?)
  • E01 (focus lost?)
This entry was posted in Summaries and tagged , , . Bookmark the permalink.