About Roger's Recipes

This is a collection of recipes or How-Tos for using CyVerse for common data analysis tasks. It is compiled by Roger Barthelson (and all the people from whom he borrowed material).

The focus will be for some of the most commonly needed functions for sequencing data analysis, which is much of what CyVerse's Discovery Environment and Atmosphere are used for.

Is CyVerse only for plant researchers? NO. CyVerse is a web-based infrastructure and is now freely available to all scientists.

INGREDIENTS	RECIPES
Your Data	How to upload your data
Your Data in the Data Store	Getting started with data analysis
Next Gen Sequencing Data	Just a quick view of sequencing data
Raw Sequencing Data	Cleaning up reads with the HTProcess Pipeline
Clean RNASeq Reads	Assembling a transcriptome
Genome Sequencing Reads	Whole Genome Assembly
Clean NGS Reads to be Mapped	Aligners available in the Discovery Environment
Some kind of file?	What is this file? What does it look like inside?
A really big batch of data (e.g. over 200 GB of files.)	You don't want to hear this...
RNASeq Reads, no genome available	RNA-Seq studies with the almond tree -- an example
Clean, microbial genome seqs, ready to be assembled	Using the SPAdes assembler...
Clean NGS Reads to be Mapped	Using the GSNAP aligner
Clean NGS Reads to be Mapped	Using the BWA-mem aligner
Many files, little time...	Parallel execution, DE style

1 Learning Materials

Roger's Recipes

About Roger's Recipes

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