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


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
File Formatting

Cloud Computing with Amazon

The Basics
Security Groups
Getting the Most Bang for Your Buck

Other Resources on the web

Next-gen data generation and Analysis

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


Software Carpentry: Programming for scientists.

General help for using the Unix Shell if you're stuck writing a pipeline or your bash script doesn't work as you expect it to this is a good forum to go to for help.