10:00a – 11:00a, 3:00p – 5:00p, 7:00p-12:30p
Goals
Deep Seq Analysis
- Analyze distribution along probe region of copy number variation
- Analyze sequence dependence of copy number variation
- If a sequence contains a deletion, do we also have that same sequence without a deletion?
- Off target binding motif analysis?
Hao Lib4 prep
- Analyze Isoform data
STORM
- image G4 cells new probes
Genome analysis
- Cufflinks data analysis
- Several key genes skipped as HIDATA.
- –max-bundle-frags
[Default is 1000000]. This is too small for GAPDH - downloading human chromosomes as separate fasta files: ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/dna/.
- Writing fasta builder to construct fasta file with only most highly expressed isoform.
STORM
- finish overnight STORM run E10rna
- Test STORM of G4. FAILED
- Test STORM of F3. FAILED
- STORM of D10. Not all nuc have obvious stains. Look more like an RNA labeling. No idea why, had good denaturing…
Ph Modeling
- Lack of change in Ph Model in response to PhM levels under diff model is Expected under the limited binding / K27 of course. Obviously if it doesn’t increase with more wt Ph it won’t increase with more mutant Ph.
- Really should move this simulations onto Odyssey. Write it such that each level/round is run on a different core and compiled at the end.