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      Fall single cell RNA sequencing workshop @ UCSF

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Introduction and Lectures
Intro to the Workshop and Core
What is Bioinformatics/Genomics Perspective?
Experimental Design and Cost Estimation
Introduction to Command-Line and the Cluster
Logging in and Transferring Files
Intro to Command-Line
Advanced Command-Line (extra)
Running jobs on the Cluster and using modules
Intro to R and Rstudio
Getting Started
Intro to R
Prepare Data in R (extra)
Data in R (extra)
Data Reduction
Project setup
Generating Expression Matrix
scRNAseq Analysis
Prepare scRNAseq Analysis
scRNAseq Analysis - PART1
scRNAseq Analysis - PART2
scRNAseq Analysis - PART3
scRNAseq Analysis - PART4
scRNAseq Analysis - PART5
scRNAseq Analysis - PART6
Guest lecture by Dr. Gerald Quon
Prepare Single Cell Alignment
Single Cell Alignment (scAlign)
Support
Cheat Sheets
Software and Links
Scripts
ETC
Closing thoughts
Workshop Photos
Github
Biocore website

Logging In & Transferring Files

You should already have an account on our systems

For Macs/Linux - Logging In

  1. Open a Terminal (usually under Applications/Utilities on a Mac), or install iterm2
  2. Cut and paste this into the terminal:

    ssh username@tadpole.genomecenter.ucdavis.edu

where ‘username’ is replaced with your username. Press Enter.

  1. Type in your password. No characters will display when you are typing. Press Enter.

For Macs/Linux - Transferring files

  1. Use scp (secure copy, a remote file copying program):

    scp username@tadpole.genomecenter.ucdavis.edu:full/path/to/file .

  2. Replace ‘username’ with your username and replace ‘full/path/to/file’ with the full path to the file you want to transfer. Note that there is a “.” at the end of the command, which is where to put the file, i.e. your current directory. You will have to type in your password.

For Windows - Logging In

Windows needs a terminal to connect with, you have a few options:

  1. Shell for Windows 10
  2. Enable SSH OR
  3. MobaXterm
  4. PuTTY

In putty, mobaxterm:

  1. Open up terminal.
  2. In the Host Name field, type tadpole.genomecenter.ucdavis.edu
  3. Make sure the Connection Type is SSH.
  4. Press “Open”. It will ask you for your username and password.

In Shell with SSH enabled:

ssh username@tadpole.genomecenter.ucdavis.edu

where ‘username’ is replaced with your username. Press Enter.

For Windows - Transferring files

  1. Open up WinSCP. If you haven’t installed it, get WinSCP here.
  2. In the Host Name field, type tadpole.genomecenter.ucdavis.edu
  3. Type in your username and password.
  4. Make sure the File Protocol is SFTP.
  5. Press “Login”.