Athurva Gore/LabNotes/2011-9-22

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Revision as of 22:27, 22 September 2011 by >Ajgore (Created page with '=TO DO= * Design LC Sciences Probes - need to analyze probes * Free space on Genome-Miner, create Shared Folder for HiSeq ** Still need to reformat Ext6T, ideally before Septemb…')
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TO DO

  • Design LC Sciences Probes - need to analyze probes
  • Free space on Genome-Miner, create Shared Folder for HiSeq
    • Still need to reformat Ext6T, ideally before September 26
  • 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 Probes

  • Designed probes for regions Dinh sent
    • Obtained 2669 probes containing at least one CpG in target, and 303 probes without CpGs in target
  • Can we further narrow down probes? Remember, we need to have multiple probes for probes with many CpGs
  • Counted CpG sites in arms; decided to allow 2 per arm pair, so no more than 4 probes per region
    • This means we need 4949 probes...too many
  • If we remove the 11 targets with the most probes, we remove 997 probes
    • This leaves us with 3866 probes; approximately 4000.
  • Should be a good set to start with at least.