All NGS/MiSeq
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Copyright © 2008, CMB Smith College |
Power Points
Cummerbund Tutorial using CuffDiff Output
Power Point from MiSeq Workshop given June 25, 2013.
Nucleic Acid and Library Prep Protocols
Protocol - Mini-Boiling RNA Prep (CWZ Lab)
NEBNext Ultra RNA Manual (for RNA library prep)
Estimating Sequencing Coverage
Converting ng/µl to nM for best cluster density on the MiSeq
Recommended Kits for Library Prep
New England Biolabs Carries Illumina compatible DNA and RNA library prep kits and Index kits with pricing
comparable to Illumina. In addition, they will give you an educational discount if using for a class. They just
recently released a magnetic bead kit for mRNA isolation from whole RNA. For most bacterial RNA applications,
you will want to eliminate rRNA. We recommend RiboZero by EpiBio for this step. For Sequencing ends-
NEB may come out with one but for right now it is Illumina's nextera_mate_pair_sample_prep_guide
The CMB is here to help with any questions you may have about making these selections.
Just contact Louie at lbierwer@smith.edu
Helpful Literature and CMB generated Bioinformatics Workflows
All NGS
How to view the quality graphs and summary in BaseSpace - SequencingAnalysisViewer_UserGuide
NGS Overview and Practical Approach to Variant Detection in NGS Data - Video. Need to download WebEx Viewer to View
DNA Seq
Post Run DeNovo Assembly Using Soap De Novo on CommandLine
Post Run DeNovo Assembly using NGen through BaseSpace
Eukaryotic Genomics Assembly and Annotation on CommandLine Jellyfish, Quake, and MakerII
Prokaryotic Genomics Assembly and Annotation using NextGene and RAST
RNA Seq
RNASeq Analysis Workflow using Tuxedo tools
RNASeq Analysis Workflow using Commandline - Tutorial
RNASeq Analysis using Tuxedo Tools on a Mason Galaxy Account
RNASeq Analysis using Rockhopper (for bacterial transcriptomes only)
RNASeq Analysis Without Reference - Article
Advanced RNA Seq Analysis Topics and Trouble-Shooting
p and q values in RNA Seq Differential Expression data
16S Metagenomics
Workflow from sample to analyzed data - uses Qiime for analysis - Tutorial
High-Speed, Multiplexed 16S Microbial Sequencing on the MiSeq® System
QIIME allows analysis of high- throughput community sequencing data
Examining the global distribution of dominant archael populations in soil
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
Links to Bioinfomatics tools
Got a question? Try asking at SeqAnswers - The Next Generation Community -It's easy to join.
DNAStar Lasergene 11- Available to use on BaseSpace but it has to be on the computer
you are using in order to view results. Google DNAStar to see all of it's capabilities.
We currently have a network license, which means we can put on any Smith computer
but only 4 can be in use at one time,so be sure you quit when you are done.
Lasergene 11 is loaded onto the AppleCart computers in the CMB - please be sure to
sign out the AppleCart if you need a computer for this purpose. Thanks
CLC Genomics Workbench - Can sign up for a 6 month free trial for having the MiSeq
UniPro UGENE - has tuxedo suite set up for RNAseq and more. Easy to use.
Galaxy - Main page - hit "user" button and register and you are good to go.
DAVID - for functional annotation
Cytoscape - Network data integration, analysis, and visualization in a box
MEGA - Molecular Evolutionary Genetic Analysis
IGV at the Broad Institute - an Integrated Genomics Viewer
Qiime - Command line program for metagenomics analysis
Links to Genome Browsers
Ecocyc - database for E.coli K12
RegulonDB - Ecoli Wiki
GreenGenes - a 16S database and workbench
IF YOU WOULD LIKE TO ADD A LINK, PAPER OR PROTOCOL TO THIS SITE, OR IF THERE IS SOMETHING MORE YOU WOULD
LIKE TO SEE ADDED TO THIS PAGE, PLEASE CONTACT LOUIE BIERWERT AT lbierwer@smith.edu THANKS