10:00 am – 12:00 am
Update on running Analysis
- Cajal and Tuck still building library, 20-40% complete.
- Won’t be done for another 24 hours at the earliest.
- maybe longer as the day brings competition of these cores and my programs are “polite” and launch at low priority.
- Interaction analysis still running, should finish before tonight
- refitting BB black D12
Internal black analysis
- D11 — conventional images useless, STORM images not promising. fortunately I already repeated this one myself
- D12 — out of focus spots are overly large
- spots also pretty dim for Alexa647
- large spots only get off-center localizations when multiple spots are called in the same frame.
- looks promising if we can refit the data.
- first pass at refitting totally mismatched files / images. Copying data, will repeat this.
- D08 — D08_08_05_2015 conventional images are more or less blank. Most STORM images very close to blank.
- D09 — data looks reasonable. Reprocessed.
- D09-10 conv looks okay, lots of storm movies missing or no reasonable data. 2-10 might be good.
- fiducial drift correction failed or extremely poor.
- Correlation based drift correction looks to be sufficient accuracy
New Stains
- D10 S1-647, D09 S3-750
- D11 S1-647, D12 S3-750
- D08 S1-647
- D10 S1-647
- E05 S1-647 + E04 S3-750
- E08 S1-647 + E07 S3-750
passaged cells, replaced media.
tossed old cells (after 2 months in culture).
For later
- E05 S1-647 + E04 S3-750
- F04 S1-647 + F03 S3-750
- L4E2 S2-647, L4E1 S3-750
Chromatin region analysis
- processing L4E17 data (15 kb of BXC)
- processing L4E17-19: 45 kb of BXC
- Need to fix G09 is a (75%) internal part of C05, not an end to end domain
- processed black 2 color data: L4E1 + L4E2.
- 750 missing in most images,
- partly due to laser off-center
- largely due to buffer death
- re-processed internal black domains as indicated above.
- some results
Attempting batch jobs on Odyssey
- see Bogdan’s email
- array launch still goes into queue
- jobs actually launched.
- individual output files and error reports also generated.
- what if we request 500 cores and then do a bunch of
system([task,' &'])commands in a loop? On a desktop these go out to separate cores. Lets see if this simple approach can work on the remote.- all java commands die with memory errors. (didn’t actually expect them all to launch, so maybe this is progress).
- actually started running all these java files. I see even _oligos.txt files for a bunch of genes, some even with data and probes.