Athurva Gore/LabNotes/2011-9-20

From ZhangLabWiki
Jump to navigation Jump to search

TO DO[edit]

  • DONE - Design LC Sciences Probes - started design script
  • DONE - CERC Paperwork - Turned in certificates
    • Need to pick up key tomorrow
  • DONE - Free space on Genome-Miner, create Shared Folder
    • Still need to reformat Ext6T, ideally before September 26
  • DONE - CMM Access Card Form - turn in tomorrow
    • Christine Domingo was not there today; try again tomorrow?
    • Email to make sure she is in the office?
  • CIRM Progress Report - due September 22nd
    • Updated CV
    • Need to write progress report section - can use already written progress report as base
  • Package Exome Scripts for Thomson Lab
  • Barcoding Padlock Probe libraries - talk to Dinh and Noi
  • Low-input Bisulfite Conversion
  • Paper with Sergio
  • Low-input Exomes (Athanasia) - analyze data?
  • Papers for Doug - ask Dr. Zhang?
  • Review GR Manuscript - by September 28

LC Sciences Probe Design[edit]

  • Probe design script finished; made a few thousand probes
    • Need to check the quality of these probes; are they usable? How many do we want to order? What is the coverage of our target sites?
    • Then, add additional targets
  • Used the probe design parameters:
our $primerMaxTm = 70;
our $primerMinTm = 50;
our $primerMaxLen=25;
our $primerMinLen=15;
#Total arm length fixed at 40 bp

our $targetMinLen=178;
our $targetMaxLen=180;

our $arewebisulfite=1;
our $using_unafold=1;
our $softwareDir='/opt/ppDesigner/src';
our $HsDir='/GenomeDB/HsGenome/hg18/';
eval `cat /opt/ppDesigner/Baylor05062011/get_probes_Baylor.pl` or die 'couldnt parse file';

  • These are slightly different than Robert's parameters for DMR330k, as primer length is smaller
  • Obtained 2972 probes from initial set

Meeting with Madhu[edit]

  • Still waiting on validation data from BGI; have confirmed ~12 de novo SNPs so far
    • BGI is taking a long time with Sanger Sequencing
  • Madhu wants to get GATK running; was having problems
    • Investigate this; subset to chr10 and run GATK on BGI's provided BAM file
    • Use two versions of GATK
    • Can we get Unified Genotyper to run? Madhu could not; showed that it either crashed with errors OR ran successfully but output no SNPs