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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.


Roger's desk

Table of Contents


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
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