Skip to content

Commit

Permalink
Fix Datahub link in FAQ (#10931)
Browse files Browse the repository at this point in the history
  • Loading branch information
jamesqo authored Aug 14, 2024
1 parent 7e4a888 commit 3569c76
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion docs/user-guide/faq.md
Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,7 @@ The TCGA PanCancer Atlas datasets derive from an effort to unify TCGA data acros

TCGA studies not sourced from GDC have the original mutation data generated by the individual TCGA sequencing centers. The source of the data is the Broad Firehose (or the publication pages for data that matches a specific manuscript). These data are usually a combination of two mutation callers, e.g. a variant caller like MuTect plus an indel caller. Note that the specific tools used and the overall process for identifying mutations can vary between centers and may have changed over time.

TCGA studies sourced from GDC use a newer version of the human reference genome, GRCh38 instead of GRCh37. For more information about the GDC data processing pipeline, see [GDC Data Processing](https://gdc.cancer.gov/about-data/gdc-data-processing). Transformations specific to our NCI-CRDC pipeline are documented in the [cBioPortal Datahub](https://github.com/cBioPortal/datahub).
TCGA studies sourced from GDC use a newer version of the human reference genome, GRCh38 instead of GRCh37. For more information about the GDC data processing pipeline, see [GDC Data Processing](https://gdc.cancer.gov/about-data/gdc-data-processing). Transformations specific to our NCI-CRDC pipeline are documented in the [cBioPortal Datahub](https://github.com/cBioPortal/datahub/tree/master/crdc).
#### What happened to TCGA Provisional datasets?
We renamed TCGA Provisional datasets to TCGA Firehose Legacy to better reflect that this data comes from a legacy processing pipeline. The exact same data is now available in TCGA Firehose Legacy studies.
#### Where do the thresholded copy number call in TCGA Firehose Legacy data come from?
Expand Down

0 comments on commit 3569c76

Please sign in to comment.