Document annotation source - Tumor Fusion Gene Data Portal

rdocking / fusebench

A workbench for aggregation and interpretation of RNA-Seq gene fusions

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Document annotation source - Tumor Fusion Gene Data Portal #15

Closed rdocking closed 7 years ago

rdocking commented 7 years ago

Please answer the following questions about the Tumor Fusion Gene Data Portal data source:

Where is it located online?
Is there an API?
Are bulk downloads available?
In general, what kinds of information are int this data source

The answers should be uploaded to the wiki in an appropriate spot.

rdocking commented 7 years ago

Where is it located online? http://54.84.12.177/PanCanFusV2/ API/Bulk downloads? Bulk download:

annotation_sources/tumour_fusion_gene_data_portal

Downloaded like so:

[2017-10-20 19:32:04]{rdocking_hs@orca01}/home/projects/hackseq17_3/annotation_sources/tumour_fusion_gene_data_portal/> wget http://54.84.12.177/PanCanFusV2/downloads/pancanfus.txt.gz

rdocking commented 7 years ago

Rough stats:

17,754 observations of 27 variables
Format has BEDPE-like information (but is not BEDPE)

rdocking commented 7 years ago

The fields included are described in the help docs:

http://54.84.12.177/PanCanFusV2/help.html

For use with the project, we should probably convert this to BEDPE as well

rdocking commented 7 years ago

'9,966 tumor samples from 33 TCGA cancer types and 689 normal samples in 19 TCGA normal tissue types were analyzed by PRADA pipeline and the realigned BAM files of RNAseq data with storage size ~35TB were generated.'
Recurrence in different tumour types is annotated, as are several different metrics