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BICF Accessing Public Data

For many types of sequencing analyses, we need access to public data stored in various databases and repositories. This workshop will discuss types of genomic reference data available through public databases such as Ensembl, NCBI, UCSC, ENCODE, and TCGA and step through how to find and download this data. The workshop will also explore how to find and download publicly available experimental data, such as data (FASTQ files and count matrices) from published papers, using GEO and the SRA repositories. While most of the workshop will access data using a web browser, downloading data from the SRA will require beginner knowledge of the command-line interface and TCGA analysis will require beginner R.


Contacts


Schedule

Topic Instructor
02/14/2020 Room E2.305
TCGA, MSigDB, PatherGO, GEO Submission
tcga slides
geo, panther, and other slides
sample data 1
sample data 2
TCGAbiolinks workshop
Spencer Barnes
SRA
ENCODE
UCSC Browser
UCSC Table Browswer
UCSC LiftOver
IGV Web APP
Holly Ruess