9:30 am – 10:15 pm
STORM
- finish overnight run
- switching still looks decent
- setup data to analyze on MORGAN.
- updated z-calibrations for both 647 and 750 parameters
- fitting bead data for drift correction
- all jobs launched before 1pm (probably need another 2 hours to finish running)
New experiments
- stained BX-C and F6 (using previous mixed sample)
- denatured at upstairs heat block at 78 (temp reasonably sensitive to adding water, use with care)
- hybridized from 10am – 7pm at 47C
- rinsed and imaging in MEA and freshly made Glox (left glox made yesterday out last night, tossed it)
- spots switching much better in 750 (Ben also fixed the TIRF)
- collecting ~55K frames 750 (30Hz, camera won’t do faster) and 65K frames 650 overnight
Ph-project
- assemble figures, send to NF
- latest complete version sent to all authors
Analysis of Green data
- mapping total reads per region
- Morgan connection got really slow
counting total reads per region
I used to use a “GenerateStrandCount” function you had written (I believe in matlab-functions).
I presume this has been replaced by “GenerateCoverageVector” or “GenerateSequenceDataStructure”?
Both of these try to find a “SequenceDictionary” field. The structure I get from BioIndexedFile on my SAM file doesn’t have this field.
I believe this is because my SAM file has no header. That pissed off cufflinks too, though I eventually got it to run. modENCODE doesn’t seem to believe in headers.
brute force approach
- using fseek to count reads, no fancy coverage vector for whole genome
- running over night
To do
- format figures into combined PDF for Ph-Polymerization paper
- Analyze Hi-C data
- Organize presentation of Green data
- Analyze two-color data