Athurva Gore/LabNotes/2011-9-23: Difference between revisions
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=TO DO= | =TO DO= | ||
* Design LC Sciences Probes | * '''Waiting for Dr. Zhang's response - Design LC Sciences Probes''' | ||
* Free space on Genome-Miner, create Shared Folder for HiSeq | * Free space on Genome-Miner, create Shared Folder for HiSeq | ||
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* Review GR Manuscript - by September 28 | * Review GR Manuscript - by September 28 | ||
=LC Sciences Probes= | =LC Sciences Probes= | ||
* Turned out I made a mistake in probe design yesterday | * Turned out I made a mistake in probe design yesterday |
Revision as of 18:29, 23 September 2011
TO DO
- Waiting for Dr. Zhang's response - Design LC Sciences 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
- Turned out I made a mistake in probe design yesterday
- Some probes were allowed to have arms longer than 40 bp total
- Redesigned probes for same targets (YX Genes [HORMAD1, ZG16] and Ecker mutation/memory that overlaps with PGP1)
- Obtained 2199 probes that captured at least one CpG and had fewer than 3 CpGs in probe arms
- Removed targets with high numbers of probes required (due to C's in arms and large size)
- Also removed 9 additional probes to make the number to order exactly 4000
- Probe Set: File:NM LC Probes Filtered 09232011.txt
- 1820 probes, with 4000 to order due to degeneracy
- Captures 14,228 CpG sites