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
* 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.
 
==PGP Data==
==PGP Data==
* Analyze merged PGP4, 6, and 10 data - need to postprocess


=Probe Design=
=Probe Design=

Revision as of 17:38, 21 September 2009

Navigation

TO DO

  • Email Sanjay Nigam - kidney methylation studies
  • Phylogenetic Tree clustering of PGP and Shendure samples
  • End-to-End Mapping with Trimming; test this approach.
  • Hemophilia - Read over CEGS proposal


Exome Resequencing

IPS and Cancer

  • 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.

PGP Data

  • Analyze merged PGP4, 6, and 10 data - need to postprocess


Probe Design

  • Baylor Probe Set is currently running on genome-tech.
  • Jay Lee Probeset
    • Need to pull out dbSNP data from snp129.txt
    • Then, need to run separate job on cDNA targets
    • Make sure conversion script still works