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
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