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BioGrids Workshops

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

Before attending a workshop, register for a BioGrids account then download and activate the BioGrids Installer software.

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1: Register for BioGrids

BioGrids Registration

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

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

Install and activate BioGrids CLI

Download and install biogrids CLI client then run: 

biogrids activate <site name>  <user name>  <activation key>

Linux

curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Linux.tgz
tar zxf biogrids-1.0.694-Linux.tgz
cd biogrids-1.0.694-Linux

OSX

curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Darwin.tgz
tar zxf biogrids-1.0.694-Darwin.tgz
cd biogrids-1.0.694-Darwin

Run biogrids

./biogrids activate biogrid-production jvinent1  70rYFTDnmCr93VUklfbf1s3M4jdyC9bFVYHew==
./biogrids install fastqc trimmomatic samtools star subread igv

Change back to home directory 

cd

Install software with BioGrids

Download and uncompress tutorial files

Run RNA-Seq workflow

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: