The following pages and posts are tagged with
| Title | Type | Excerpt |
|---|---|---|
| Cell Ranger | Page | Cell Ranger is the command-line software for preprocessing raw sequence data from a 10X single cell sequencing experiment. The output from Cell Ranger os a ... |
| Project management and quality assurance for RNAseq projects | Page | Managing your RNAseq project and checking the quality of raw data are essential first steps in the analysis of any RNAseq experiment. The protocol below out... |
| Depositing RNAseq data to GEO | Page | This page will walk you through the steps to make your data publicly available so you can meet the requirements for manuscript submission and publication |
| RStudio Server | Page | How to access RStudio through your web browser |
| Metagenomics in the cloud | Page | This 4 hour workshop takes users through setting up their own cloud computer, intalling a Snakemake-based pipeline called Sunbeam for analysis of shotgun met... |
| Kallisto | Page | Kallisto is our first choice for aligning reads because it combines speed, accuracy, and the ability to leverage bootstraps for modeling technical variance |
| CHMI linux server | Page | CHMI maintains a custom configured compute server that runs Linux Ubuntu 18.04 LTS. This machine has two 6-core Intel Xeon E5-2643v4 CPUs (12 cores total), ... |
| Preparing microbiome data for deposit to microbiomeDB.org | Page | Instructions on how to prepare your raw sequence data and metadata mapping file for submission to microbiomeDB.org |
| analysis of 16S rRNA gene sequencing data | Page | Preparation of V4 region, 16S dual-indexed libraries for sequencing on an Illumina platform |
| QIIME2 workflow | Page | Using the Quantitative Insights Into Microbial Ecology (QIIME2) software pipeline for analysis of marker gene-based microbiome sequencing data |
| Bioinformatics Software | Page | A summary of the bioinformatics software currently installed on our Linux cluster. |
| Exploring WGS and Metagenomic data using minHash sketches | Page | QC and analysis of microbial WGS and metagenomic data using Sourmash |