The page is a central reference of information and notes for computational biologists and software engineers in the CGA group, as we transition from the TCGA era of GDAC to the GDC/GDAN era. As of July 2016, the Genomics Data Commons has replaced the TCGA Data Coordination Center as the repository of not only TCGA data but also for other existing genomics projects (such as TARGET), as well as future genomics projects.
Reference Data
- For GDAN pipelines we will store on-premises reference data in
/xchip/cga/reference/GDAN The first entry in this directory was taken from /cga/tcga-gdac/hailei/FH/miRSeqpreprocess and moved to
./GDAN/miR/miRSeqpreprocess/mature.21.fa.gz because reference data should persist in locations free of individual usernames.
This data is used by the miRSeq preprocessing pipeline to filter miRs.