Oct 29, 2018:
Just a reminder that PDC has issued an alpha of it's MVP release. Would be nice to have more Broadies take a look. Presently supports only CPTAC2 data.
- iCoMut:
- undergoing update for UCEC AWG
- FYI: HG38 mutation calls underway by WashU (slated for 11/8 V2 freeze)
- waiting for Broad example data to add new proteomics tracks
- undergoing update for UCEC AWG
- HG38: progress, GDCtools config file needed
- CN data:
/xchip/gdac_data/cptac3/genomic_data_mirror/CPTAC3_WashU_hg38/UCEC/WXS_CNV_hg38_v1.0_20180809
But what is more biologically important: WGS for CN or HG38?
Because at present only VCFs available for WGS CN data
- CN data:
- LUAD: new proteomic data "in progress," but in "new location" @ DCC:
- per this email exchange
Changed from/to:
8_CPTAC3_Lung_Adeno_Carcinoma/LUAD_mzML/
8_CPTAC3_Lung_Adeno_Carcinoma/A_CPTAC3_hg38_CDAP/LUAD_mzML/
Per Nathan: "The files under A_CPTAC3_hg38_CDAP represent the re-run of the CDAP
analysis for files analyzed before the release of Broad's new
RefSeq/hg38 protein sequence database and any new ones going forward."
...
Recap of last week's F2F:
Good FireCloud workshop attendance & feedback
Proteomic:
Genomic:
GDC has made progress automating their pipelines
CPTAC genomic data will be HG38 going forward;
Phased delivery CCRC & UCEC first, to allow publications to be in pipeline by next funding cycle (Gantt chart)
- Two special journals in Fall 2018:
- Special issue Mol. Cell Proteomics:tools, algorithms & computational methods
- Submission deadline will be in November, 2018
- Submission deadline will be in November, 2018
- Journal of Proteome Research: Software Tools and Resources
- Submission deadline September 14, 2018
- Special issue Mol. Cell Proteomics:tools, algorithms & computational methods
- FOA: Sustained Support for Informatics Resources for Cancer Research and Management (U24)
- Due June 14
- Submit LOI by May 14
- Letters of support: gathering now
- Time Permitting: genomic pathway analyses
- GDAN Lung pathifier analyses
- iCluster: Hailei
...