Welcome to YeoLab/welcome’s documentation!

Getting started (everyone)

• Getting Started
  • Sanford Internet Access
  • Printing
  • Reserving rooms in SCRM building
  • Access to Compute Environments
  • Online Resources
  • Internal Resources
• Lab meeting etiquette and protocols
  • For speakers
  • For the audience

Getting started (wetlab)

Check out this google doc on our wet lab practices.

Getting started (drylab)

Set up your computer for drylab development

1. First thing you’ll want to do is get an account on TSCC. Email Jim Hayes and ask to be added to the groups yeo-group and scrm-group.
2. If you don’t have a Github account yet, go make one.
3. Ask to get added to the YeoLab group on Github.

5. Install the Anaconda Python Distribution to your laptop. (Get Python 2.7 for now)
6. Install PyCharm (Community edition is fine).

TSCC

Next, here are the TSCC-specific setups. This is pretty big so it’s a separate page.

• TSCC
  • Important rules
  • First Steps
  • IPython notebooks on TSCC
  • Installing and upgrading Python packages
  • Installing R packages (beta!)
  • Submitting and managing compute jobs on TSCC
  • Random notes
  • Running RNA-seq, CLIP-Seq, Ribo-Seq, etc qscripts GATK Queue pipelines
  • Combining outputs from the pipeline into matrices

Create flotilla inputs

Here is an example IPython notebook of scripts to create flotilla inputs. (really should be a few scripts in gscripts, but that will come later)

Uploading to GEO

When uploading to GEO

• How to upload files to GEO
  • Preparing to upload to GEO
  • The actual uploading: FTP Transfer to NCBI
  • Telling NCBI you uploaded stuff

Indices and tables

• Index
• Module Index
• Search Page