Athurva Gore/LabNotes/2009-9-21: Difference between revisions

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{{ AGLabEntry|2009-8-18|2009-8-22 }}
{{ AGLabEntry|2009-8-18|2009-8-22 }}
=TO DO=
=TO DO=
* Analyze merged PGP4, 6, and 10 data - need to postprocess
* Email Sanjay Nigam - kidney methylation studies
* Email Sanjay Nigam - kidney methylation studies
* Phylogenetic Tree clustering of PGP and Shendure samples
* 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==
==IPS and Cancer==
* Check new DF699 and Foreskin Fibroblast Data
* Check new DF699 and Foreskin Fibroblast Data
** Very few reads present; probably not going to be able to draw anything from this.
===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
** Need to pull out dbSNP data from snp129.txt
** dbSNP Probes are done
** Then, need to run separate job on cDNA targets
** 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

Navigation[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?