Athurva Gore/LabNotes/2009-9-21: Difference between revisions
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>Ajgore (New page: {{ AGLabEntry|2009-8-18|2009-8-22 }} =TO DO= * Analyze merged PGP4, 6, and 10 data - need to postprocess * Email Sanjay Nigam - kidney methylation studies * Phylogenetic Tree clustering of...) |
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{{ AGLabEntry|2009-8-18|2009-8-22 }} | {{ AGLabEntry|2009-8-18|2009-8-22 }} | ||
=TO DO= | =TO DO= | ||
* Email Sanjay Nigam - kidney methylation studies | * Email Sanjay Nigam - kidney methylation studies | ||
* End-to-End Mapping with Trimming; test this approach. | * End-to-End Mapping with Trimming; test this approach. | ||
* Hemophilia - Read over CEGS proposal | * Hemophilia - Read over CEGS proposal | ||
=Exome Resequencing= | =Exome Resequencing= | ||
==IPS and Cancer== | |||
* Check new DF699 and Foreskin Fibroblast Data | * Check new DF699 and Foreskin Fibroblast Data | ||
===AL001 Set=== | |||
* Very few reads present; not able to draw anything from this. | |||
===AL002 Set=== | |||
* New set, contains Foreskin-DF699 pair and CraigVenter-IPS pair | |||
* Need to run analysis; do we need to trim? | |||
** Check this. | |||
* Currently running on genome-miner:/media/TmpStore2 (TmpStore1 is low on space, need to delete some of the old not-working analysis) | |||
==PGP Data== | |||
* Analyze merged PGP4, 6, and 10 data - need to postprocess | |||
* Phylogenetic Tree clustering of PGP and Shendure samples | |||
=Probe Design= | =Probe Design= | ||
* Baylor Probe Set is currently running on genome-tech. | * Baylor Probe Set is currently running on genome-tech. | ||
* Jay Lee Probeset | * Jay Lee Probeset | ||
** | ** dbSNP Probes are done | ||
** | ** Need to run separate job on cDNA targets | ||
** Make sure conversion script still works | ** Make sure conversion script still works...check if we can add the same values? |
Latest revision as of 23:51, 21 September 2009
[edit]
TO DO[edit]
- Email Sanjay Nigam - kidney methylation studies
- End-to-End Mapping with Trimming; test this approach.
- Hemophilia - Read over CEGS proposal
Exome Resequencing[edit]
IPS and Cancer[edit]
- Check new DF699 and Foreskin Fibroblast Data
AL001 Set[edit]
- Very few reads present; not able to draw anything from this.
AL002 Set[edit]
- New set, contains Foreskin-DF699 pair and CraigVenter-IPS pair
- Need to run analysis; do we need to trim?
- Check this.
- Currently running on genome-miner:/media/TmpStore2 (TmpStore1 is low on space, need to delete some of the old not-working analysis)
PGP Data[edit]
- Analyze merged PGP4, 6, and 10 data - need to postprocess
- Phylogenetic Tree clustering of PGP and Shendure samples
Probe Design[edit]
- Baylor Probe Set is currently running on genome-tech.
- Jay Lee Probeset
- dbSNP Probes are done
- Need to run separate job on cDNA targets
- Make sure conversion script still works...check if we can add the same values?