workshops

BioGrids Workshops

Learn how to use the BioGrids Installer with practical science applications.

To attend a workshop register for a BioGrids account and download the BioGrids Installer software.

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1: Register for BioGrids

2: Install BioGrids

OSX CLI:
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Darwin.tgz

Linux CLI:
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Linux.tgz

3: Activate BioGrids

CLI Substitute your sitename, user name and activation key:

./biogrids activate [site name] [user name] [activation key]

Example:

./biogrids activate biogrid-production jvin1 70rYFBTDnr93VUklfbf1s3M4jdyC9bFVYHew==

GUI Fill in the form when prompted upon first start of the BioGrids application.

Workshops

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Using BioGrids for RNA-Seq on AWS and Your Laptop

May 15, 2019 - 10:30am | TMEC 106 | Register Here

Complete workshop data files and scripts: biogrids_workshop.tar.gz

Download then uncompress:

curl -kLO https://biogrids.org/wiki/downloads/biogrids_workshop.tar.gz
tar zxf biogrids_workshop.tar.gz
cd biogrids_workshop
./runMOV10.sh ./raw_fastq/ENCODE_MOV10.fq

View results with IGV:

igv

Within IGV:

1: Genomes / Load Genome from File... (chr1_MOV10.fa)

2: File / Load from file... (chr1_MOV10.gtf)

3: File / Load from file... ( .bam file)

Genome Resources

ENCODE data files can be found here for CalTech RNA-Seq : http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/

Use this bam file: wgEncodeCaltechRnaSeqK562R1x75dAlignsRep1V2

Region of MOV10 gene: chr1:113,214,934-113,243,900

How to download whole genome:

• UCSC ftp site: hgdownload.cse.ucsc.edu
• UCSC web site: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/
• UCSC recommends using an ftp client for large file downloads
• chr1 is only 70M

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