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Lab 11 Broad Firehose

Lab 11 Broad Firehose. April 15/16, 2014 Lin Liu Yang Li. Broad Firehose. Broad. Firehose. TCGA The Cancer Genome Atlas. The Cancer Genome Atlas (TCGA): a project, begun in 2005, to catalogue genetic mutations responsible for cancer, using genome sequencing and bioinformatics.

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Lab 11 Broad Firehose

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  1. Lab 11Broad Firehose April 15/16, 2014 Lin Liu Yang Li

  2. Broad Firehose Broad Firehose

  3. TCGAThe Cancer Genome Atlas The Cancer Genome Atlas (TCGA): a project, begun in 2005, to catalogue genetic mutations responsible for cancer, using genome sequencing and bioinformatics. http://cancergenome.nih.gov/

  4. TCGAThe Cancer Genome Atlas

  5. TCGAThe Cancer Genome Atlas The project scheduled 500 patient samples, more than most genomics studies, and used different techniques used to analyze the patient samples. Techniques gene expression profiling, copy number variation profiling, SNP genotyping, genome wide DNA methylation profiling, microRNA profiling, and exon sequencing of at least 1,200 genes. The TCGA is sequencing the entire genomes of some tumors, including at least 6,000 candidate genes and microRNA sequences.

  6. TCGAThe Cancer Genome Atlas https://tcga-data.nci.nih.gov/tcga/tcgaAnalyticalTools.jsp

  7. TCGAThe Cancer Genome Atlas https://tcga-data.nci.nih.gov/tcga/tcgaAnalyticalTools.jsp

  8. Broad GDAC Firehose Broad Institute's Genome Data Analysis Center (GDAC): On behalf of The Cancer Genome Atlas, we've designed and operate scientific data and analysis pipelines which pump terabyte-scale genomic datasets through scores of quantitative algorithms, in the hope of accelerating the understanding of cancer.

  9. Broad GDAC Firehose

  10. Broad GDAC Firehose Download Firehose Data:

  11. What data can you download? Mutation calling, classifying, summarizing and significance-testing Copy number alteration detection and significance-testing Expression- and methylation-based clustering Associating genomic data with common clinical, treatment or survival groups

  12. So, firehose has processed data already • GISTIC, MutSigCV etc • Exercises: • How to get all the MutSig results for ovarian cancer? • ./firehose_get -tasks mut analyses latest ov • unzip file gdac.broadinstitute.org_OV-TP.MutSigNozzleReportCV.Level_4.2014011500.0.0 • Check OV-TP.final_analysis_set.maf

  13. Broad GDAC Firehose Firehose Documentation: https://confluence.broadinstitute.org/display/GDAC/Documentation

  14. Side issues: how to access TCGA bam files https://cghub.ucsc.edu/ http://www.ncbi.nlm.nih.gov/gap

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