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Table of Contents Update Genomes Array Technology Next Generation Sequencing DNA-Seq RNA-Seq Illumina HXB Parentals= Universal Human Reference= Helicos Sanger Institute Tools Git Wiki Gene Identifier Conversion Tools Cytoscape Basic Linux/Unix Commands PhantomJs Inkscape Genetools Sequence Ontology Project Camtasia Software for managing Genomic Intervals PLINK Glossary

Update Genomes

Steps to update Rat Genome

Steps to update Mouse Genome

Array Technology

3' Arrays

Exon Arrays

Next Generation Sequencing

DNA-Seq

• HxB Parentals - DNA
• SNPs and Indels using samtools/bcftools
• Indel Detection using Ad Hoc Methods
• The Effect of Variants on Coding Genes

RNA-Seq

Illumina

HXB Parentals=

• Total RNA Illumina
• PolyA mRNA Illumina
• Small RNA
  • Trimming and Post-processing-Small RNA
  • Small RNA Alignment, Filtering, and Annotation
  • Female and Male Rat Brain Small RNA Data Analysis in 10 Days

Universal Human Reference=

• Total RNA Illumina
• Strand-Specific Total RNA Illumina

Helicos

• Helicos Track on the Phenogen Site

Sanger Institute

• C57 and DBA Sanger Brain RNA Seq

Tools

Git

Information about Git including Git Clients

Wiki

Information about Wiki

Gene Identifier Conversion Tools

Gene Identifier Conversion Tools

Cytoscape

Cytoscape Layout Algorithms

Basic Linux/Unix Commands

Basic Linux Unix Commands

PhantomJs

PhantomJs Website

Using phantomjs you can make a png, pdf, jpeg or gif file from a Url that displays an SVG file.

cd /Users/clemensl/phantomjs/phantomjs-1.7.0-macosx/bin
./phantomjs ../examples/rasterize.js http://ariya.github.com/svg/tiger.svg tiger.png

This creates a png file:

Inkscape

Inkscape website

Inkscape is an open source vector graphics editor. One thing Inkscape can do is convert svg files to other formats.

Genetools

Genetools

Sequence Ontology Project

Sequence Ontology Project

Camtasia

Camtasia Web Site

Camtasia is Screen Recording and Video Editing Software

Software for managing Genomic Intervals

GenomicFeaturesAndRanges

GenomicRangesExample

PLINK

PLINK

Glossary

Glossary