Athurva Gore/LabNotes/2011-9-20
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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
- Designed probes: File:NM LC Probes 09172011.xlsx
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