10:00 am – 8:00pm
10 am – 11 am: Ph simulations
- migrating Ph simulations onto Morgan.
- running Ph simulations
- maybe much shorter equilibration time and just many more rounds of simulation would be better
- running lots of short simulations across a broader range of Ph. This round wont finish before tomorrow.
11:00 am – 12:45 am
- revising MERFISH proofs
MERFISH meeting and probe design 1pm – 5pm
- 20mers 66C – 76C not enough
OligoArray batch launch issues
- read-write speed of fasta files seems to be limiting new launch — 30 jobs quickly launched but none complete
- troubleshooting OligoArray speed
- at crosshybeT of 99, still get lots of ‘nonspecific oligo ignored at this time. Later get
- launched a 40 to 50% GC content version of scan (this is going to get less than 1000 genes) [no other stringency parameters]
- launched a 15 to 75% GC content (this isn’t much of a cut).
- stopped previous 20 mer building at 35869 of 37442 probes. (lib11 prep folder: 15-04-03_Probes_20mers_t66Cx99Cs99C).
Probe numbers
- Previous 30mers, FPKM > 0.1 and >100 probes = 2197
- New 20mers, FPKM > 0.1 and >100 probes = 3929
- Previous 30mers, FPKM > 1 and >100 probes = 1856
- New 20mers, FPKM > 1 and >100 probes = 3026
- New 20mers, FPKM > 1 and >50 probes = 6920 (4 2ndaries per probe we still have 50 per hybe).
- New 20mers cuts: Tm 66 to 76.
- Of 37608 genes in our database, 12,016 are longer than 2 kb (i.e. 100 probes if we just uniformly tile with 20mers). Not sure why I am losing so many…
5pm – 8pm: more Ph simulations
- need to explain limited binding sites (K27 model) and its effects on cluster size distribution.
- I think actually binding is too strong, data suggests there are fewer