SETAC-NA 2018 RNAseq workshop (Nov. 4, 2018)
=================

Workshop website: https://setac-omics.readthedocs.io/en/latest/index.html

This is a collaborative note-taking document, hosted by [hackmd.io](https://hackmd.io/). Notes can be written in [markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) and exported later to `.pdf`, `.html`, or `.txt`. This document is live! After the workshop, we will lock it for editing, but the notes will be preserved. So, feel free to ask questions, take notes here. We will do our best to fill in answers and links as we go along so you will have them in this one document later.

## During the workshop, discuss with your neighbor (10 min):

* Name,
* Where you're from (institution)
* What organism(s) you work with
* How long did it take you to travel here?

## Workshop Sign-in:

1. Renee Jordan, Northern Arizona University (Flagstaff, AZ), ninespine stickleback, 6 hours.
2. Dani Cucchiara, University of Flcd ..orida, Gainesville, Florida, Daphnia magna. About 6 hours.
3. Monika Roy , UMass Amherst, Zebra Fish, 8 hours
4. Susari Malala Irugal Bandaralage, University of Saskatchewan, Saskatoon, Canada, fathead minnows, about 9hrs
5. Ulyana Fuchylo, University of Saskatchewan, Fathead minnows, 7hrs
6. Sarah Wallace, Institut National de la Recherche Scientifique (Quebec City, Canada), double-crested cormorants,12h+
7. Lisa Johnson, UC Davis, killifish & microbial euks & marine inverts, 20 min

7. Carly Colville, U. of Saskatchewan, fathead minnow, 4 hours+
8. Paige, UC Davis, Delta Smelt, 15 minutes!
8. Ève Gilroy, Environment and Change Canada (Burlington ON Canada), freshwater snails, 14+ hours
9. Candice Lavelle, US EPA Gulf Ecology Division. Fish and amphibians species but mostly fathead minnows and xenopus laevis currently. 8 hour flight.
10. Nicole Hack, California Water Resources Control Board - Office of Information Managment and Analysis, mostly fish, 15 min bike ride
11. Phil Ankley, University of Saskatchewan, Rainbow Trout/Fathead Minnow, 6 hours
12. Marie Noel, Ocean Wise Conservation Association, Vancouver BC, 2 hours, killer whales, beluga whales and harbour seals.
13. Casey Lindberg, Duke University (Durham, NC), Atlantic killifish and Zebrafish, 7ish hours
14. Artem Krasnobaev, Wageningen UR, 12 hours, Limpets

## Jetstream login info:
https://use.jetstream-cloud.org/application
Creating a computer which acts as a cloud instead of working locally.

**Username:**
dibbears

**Password:**
davis9.2018

*This log-in will work for up-to one year (Nov 2019)
*for US only
instance = "starting someone else's computer" or a "cloud"
use allocation code that ends in -142
## Questions

## Bioconda
An environment with a community of bioinformatics that make installing all the software easier.

* Has version control
* can use bioconda to "freeze" an environment to save your analysis code for what softwares you are using
* can use bioconda to create a new environment to work in

## Bash
Bash means "born again shell". An agnostic program meaning it doesn't know what you want it to do.
* sudo
* echo = print
* ls = files and folders in your current directory
* man = manual with help file on following command
* "> .txt" = to pipe to text file
* cat = open a file to see contents
* pwd = print working directory
* mkdir = make new directory
* rmdir = removes a specific directory
* rm -rf = removes a directory and all contents - be cautious!
* | = pipe
* zcat GCF_000826765.1_Fundulus_heteroclitus-3.0.2_rna.fna.gz | grep -c "^>" = count how many lines have > at a beginning of a line
* zcat GCF_000826765.1_Fundulus_heteroclitus-3.0.2_rna.fna.gz | grep "^>" | head -n 20 = print out first 20 lines with this "pattern"
* zcat GCF_000826765.1_Fundulus_heteroclitus-3.0.2_rna.fna.gz | grep -v "^>" | wc -m = remove lines with the "pattern" (so the titles) then count how many words (nucleotides) = size of transcriptome in file

## Rstudio
A way to graphically interact with the files that are stored on the cloud.

We want our quality scores to be as close to 40 as possible.

Illumina maximum length of a sequence is ~150bp. Trying to go over this means your reads may be inaccurate.

## Differential expression
* Around 15M reads for RNASeq per individual is enough.
* For de novo, need more like 100M.
* Watch programs for if you have to normalize data beforehand or not.

## Links

* [markdown cheatsheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)

## Extra Jetstream Instances

(If you use one, please put your name next to the IP address below so someone else does not use the same instance.)

* Backup1, 149.165.170.67
* Backup2, 149.165.170.196
* Backup3, 129.114.17.54
* Backup4, 129.114.104.6
* Backup5, 149.165.171.51
* Backup6, 129.114.16.112
* Backup7, 129.114.16.108

## Practice markdown

block of code:

cat filename > filename2

## Enter your own notes here!

#grep -c (How many of)

## Enter two absolute directories here..
/home/dibtiger/Downloads/
cd ../Music/
cd ../Public/
/home/dibbears/Music/
/home/dibbears/Public/
../Downloads/
/home/dibbears/Downloads
/home/dibbears/Pictures/
/home/dibbears/R/
/home/dibbears/Downloads/
dibbears@js-16-123:~/Downloads$
/home/dibbears/Downloads
dibbears@js-16-123:~/Videos$
cd /home/dibbears/Videos/
cd /home/dibbears/R/
/home/dibbears/Downloads
/home/dibbears/Public/
/dibbears@js-16-123:~/Videos$
/home/dibbears/Templates
/home/dibbears/Desktop
/home/dibbears/R
/home/dibbears/Music/
home/dibbears/Pictures/
/home/dibbears/Templates/
home/dibbears/Templates
home/dibbears/Downloads
/home/dibbears/Public/