Welcome to Data Carpentry Genomics Workshop at University of Nevada, Reno!
===

This website contains materials for the [Data Carpentry Genomics Workshop at University of Nevada, Reno](https://sateeshperi.github.io/2019-01-15-reno/) two-day course (9:00 am-5:00pm), held on 15-16th January, 2019 at the [Mathewson-IGT Knowledge Center - 107](https://library.unr.edu/).

We are very excited to have you here and hope that we can get through a lot of material by the end of the workshop.

This workshop runs under a [Code of Conduct](code_of_conduct.html). Please respect it and be excellent to each other!

Twitter hash tag: #DCUNR

Notes from the course:

[Hackmd.io](https://hackmd.io/7MqCeQo3RnqMDiZMZBXi7Q#)

## Instructors

* [Elias Oziolor](https://oziolor.wordpress.com/)
* [Sateesh Peri](https://sateeshperi.github.io/)

This workshop incorporates materials from the [Analysis of Next Generation Sequencing or ANGUS](https://angus.readthedocs.io/en/2018/) and several nonmodel RNAseq workshops. We recommend you visit and explore these materials! ANGUS materials are taught at the [Data Intensive Biology Summer Institute or DIBSI](http://ivory.idyll.org/dibsi/) coordinated at UC Davis every summer by [Dr. Titus Brown](http://ivory.idyll.org/lab), which Elias and Sateesh assist with in their capacity as certified [Carpentry Instructors](https://software-carpentry.org/blog/2017/09/merger.html).

## Schedule in brief

**Day-1**

 09:00-09:45am [Introduction and Genomics Workshop Overview](https://unr-omics.readthedocs.io/en/latest/intro.html)

 09:45-10:30am [Introduction to CyVerse Atmosphere Cloud](https://unr-omics.readthedocs.io/en/latest/Logging_on_Atmosphere_Cloud.html)
 
 10:30-10:45am  Coffee/Tea break

 10:45-12:00pm [BASH- Command Line for Genomics](https://unr-omics.readthedocs.io/en/latest/bash_lesson.html)

 12:00-1:30pm  Lunch Break (lunch will be provided!)

 01:30-2:45pm  BASH - continued & [Bioconda](https://unr-omics.readthedocs.io/en/latest/bioconda-config.html)

 02:45-3:00pm  Coffee/Tea Break

 03:00-4:00pm [RNAseq overview and Trimming sequencing data](https://unr-omics.readthedocs.io/en/latest/quality-trimming.html)  

 04:00-5:00pm [Version control with Github](https://unr-omics.readthedocs.io/en/latest/git_lesson.html)

 **Day-2**

 09:00-10:30am [Transcriptome Assembly](https://unr-omics.readthedocs.io/en/latest/transcriptome-assembly.html)

 10:30-10:45am  Coffee/Tea Break

 10:45-12:00pm  [Read Quantification](https://unr-omics.readthedocs.io/en/latest/rnaseq-quant.html)

 12:00-1:30pm  Lunch Break (lunch will be provided!)

 01:30-2:30pm  [Differential Expression](https://unr-omics.readthedocs.io/en/latest/DE.html)

 02:30-2:45pm  Coffee/Tea Break

 02:45-5:00pm  Project Organization and Markdown

## Other info

* These lessons are based on the original [Eel Pond Protocol](https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/index.html), then [edited in 2016](https://eel-pond.readthedocs.io/en/latest/) and [automated](https://github.com/dib-lab/eelpond) by Dr. Tessa Pierce.
* Two other nonmodel RNAseq workshops: [DIBSI 2017](https://dibsi-rnaseq.readthedocs.io/en/latest/) and [SIO-BUG 2017](https://rnaseq-workshop-2017.readthedocs.io/en/latest/index.html)
* [Backup files](backup.html), if something goes wrong
* If you find that you would like more practice working on the command line, here is a [command-line bootcamp](http://rik.smith-unna.com/command_line_bootcamp/?id=yk822u2rpo). In addition, BASH training videos are freely available through the [NH-INBRE program, the UNH Bioinformatics Core facility](http://nhinbre.org/bioinformatics-modules/).
* Source documents for these lessons can be found on [GitHub](https://github.com/WhiteheadLab/2018-setacna-rnaseq/).