TCGA - GSC-GCC Pipeline Reporting

[GoogleCodeExporter]

Determine additional requirements from TCGA per discussions 05/10/11.

- Modify Geneus to capture data (Dennis)
- Provide prior information to populate database (Dan)
- Populate database with necessary information ???
- Implement in R pipeline and create/modify scripts to retrieve info from 
Geneus(Fei)

TCGA deadline two weeks from today.

Original issue reported on code.google.com by dmagli...@gmail.com on 11 May 2011 at 6:28

[GoogleCodeExporter]

Dan to provide excel sheet with batch IDs going back to batch 1, and date of 
receival.

Specs: See GSC-GCC Pipeline Reporting - TCGA Members - National Cancer 
Institute - Confluence Wiki.pdf for specs.

Dates to keep track of will include date of bisulfide conversion (or QC date if 
bisulfide date is missing) and date packages were created (which is one day 
after samples have been processed in the lab).

Disregard R pipline implementation per Fei. Since this is an internal/TCGA 
report not intended to be shared or made public, use any scripting tool to 
complete in most efficient way.

Original comment by dmagli...@gmail.com on 11 May 2011 at 4:48

[GoogleCodeExporter]

- Best method for completion would be to use Geneus's report system since this 
is not a regular pipeline issue. We already record dates, batch IDs, etc. so we 
just need to create the report using their system.

Alternative would be to use Zack's Geneus dump using his perl script and XML 
transform per email titled "Mapping plate well position to bead array position, 
and more" dated 5/11/11.

Original comment by dmagli...@gmail.com on 13 May 2011 at 9:52

[GoogleCodeExporter]

Because kits used for bi-sulfite conversion can be used on different days, 
first day of use is used as conversion date. To be done by hand until 
automation of TCGA packaging is resolved. Created scripts for formatting dates 
in case of excel mangling. Next due date Aug 10.

Original comment by dmagli...@gmail.com on 27 Jul 2011 at 11:40

• Changed state: Done

[GoogleCodeExporter]

Per Tim: For posterity, methylumi now extracts all protocol data from the 
IDATs. However, this only extends to factory decode dates and USC scan dates, 
so bis conversion may need to be manual forevermore.

header and first line:

Batch   Date Received   Intended Platforms  Intended Data Types Reference 
Genome  Completion Date Qualifier   Completion Date Qualifier   ABBR    Notes
1   2007/4/23   GoldenGate; HM27    DNA Methylation NCBI 36.1   2008/6/18   Bisulfite 
Conversion  2008/6/19   Data Package Created    GBM 

Original comment by dmagli...@gmail.com on 28 Jul 2011 at 5:03