Tuesday 02/25/14

11:00a – 11:30p

Data compression (~11a-12p)

• troubleshooting beaddax averaging
• added some safety checks.
  • System now checks to see if detected files for deletion contain the downsampled ds tag. If they do they won’t be deleted.
  • System also checks if 561 target file to be deleted has a corresponding ds60 tagged downsampled file before deleting.
  • Added a try catch continue to bead-averaging. Rare movies give daxread errors for reasons I don’t yet understand. We just skip these and go on. The safety checks added above should preserve the original movie.
• Code running smoothly, freeing up many TBs of data on ProBox.

Library 3 prep (~12p – 4p)

• OligoArray troubleshooting
  • Want to kill BLAST jobs that hang, don’t kill java jobs, these will recover as you kill the BLAST.
  • Updated this in the OligoArray batch launcher function
  • This pipeline is getting smoother. Probably ready to start moving to its own functions.
• Final checks for Library 3
  • anti-sense transcription checks out.
  • a few spot-checked probes align to correct targets with less than full 42 bp (e.g. 32). Seems to be a genome seq mismatch or something?
• Ordering Library 3
  • Library design looks good, submit as Pending Order to get a PO. Then we send that to Marcelo along with the Fasta
  • converted space/tab separated primer data tables (Matlab, why is the default space-delimited instead of tab-delimited? Or LibreOffice at least thinks its just space delimited?)
  • fixed small bug in column headings
  • Submitted primer plates as IDT wishlist, Email to Alec, and entry on Pending Orders.

Deep Seq Error analysis (~4p – 6p)

• using Jeff’s CIGAR parser
• Overall looks pretty good
• why do deletions increase steadily across the sequence body?
• see post

Cell culture

• passage cells (should restart from stock!)

Analysis of multi-color data (~6p – 11p)

• high background 🙁
• data-sets need organization
• let’s tackle this more tomorrow