Athurva Gore/LabNotes/2011-9-22: Difference between revisions
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>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…') |
>Ajgore |
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** This leaves us with 3866 probes; approximately 4000. | ** This leaves us with 3866 probes; approximately 4000. | ||
* Should be a good set to start with at least. | * Should be a good set to start with at least. | ||
* Probe Information File: [[File:NM_LC_Probes_Filtered_09222011.txt]] |
Latest revision as of 22:38, 22 September 2011
TO DO[edit]
- 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[edit]
- 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.
- Probe Information File: File:NM LC Probes Filtered 09222011.txt