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**Cartwright lab Unix and Next-gen Sequencing Wiki**
Here you can find a collection of resources for next-gen data analysis in Unix-like environments. All information and software on these webpages are distributed under the Creative Commons Attribution license version 3.0 or higher.

Please use the **discussion** section to post questions or announcements and initiate conversations.

Bench Work
**Protocols for Next-Gen Sample Prep and Library Construction** **Sequencing Centers**

Basic Unix tools and commands
**Unix Commands** **Working with Archived and Compressed Files** **Killing Processes** **Installing Programs**

Job control and useful trickery for writing your own pipelines
**Input/Output Redirection** **Running Long Jobs**

Editing text files using Text Wrangler and Sed
For a quick reference check out these **sed one liners** !
 * Editing Text Files **

**The basics of working remotely**
**Working on Remote Machines** **Computing Resources on Campus**

**Tutorials**
Michigan State University's ** next-gen course ** also has a website with** tutorials **. **Getting Started With Next-Gen Data** **RNAseq Assembly in Trinity** **DNAseq Assembly in Velvet** - TO UPDATE **Differential Gene Expression with DESeq** **Differential Gene Expression Python Pipeline** - TO UPDATE **Orthology Assignment** - TO UPDATE **Calling SNPs in Next-gen Data** - TO UPDATE **Analyzing Barcode Data in SPIDER** **Setting up an FTP server on a Mac** **Mapping with BWA and Bowtie** - TO UPDATE

Analysis Tools

 * Scripts ** - TO UPDATE
 * BLAST ** - TO UPDATE
 * File Formatting **

Cloud Computing with Amazon
**Getting the Most Bang for Your Buck**
 * The Basics **
 * Security Groups **

**__Next-gen data generation and Analysis__**

 * SeqAnswers **: Very active and useful forum for those concerned with generating and analyzing next-gen data.