Prep Work #4 - Conda, scp, IGV, and Plotting in R

Learning Objectives

  1. Continue practicing Unix on MARCC
    • Install programs with conda
    • Create a metagene with deepTools
  2. Practice transfering files from MARCC
  3. Install IGV
  4. Continue practicing plotting using R

Tasks

  1. Install programs using conda and test deepTools
    • Connect to MARCC via ssh
    • Follow these instructions

    • Log out of MARCC (or use a different terminal). Transfer metagene plot from MARCC to local computer to view image (scroll right to see entire command … ends in Desktop/PG2018)

      scp username@jhu.edu@gateway2.marcc.jhu.edu:scratch/prepwork/k4.png Desktop/PG2018
    • Submit k4.png to your TA
  2. Install IGV
    • Install the IGV 2.4.10 Mac App or Windows Zip (not Launch icon)
      • Install Java v1.8 if not already installed (not 1.7 or 1.9)

    • Transfer bigWig file using scp (scroll to see entire command)

      scp username@jhu.edu@gateway2.marcc.jhu.edu:work/roadmap/HUES64_rep1.mRNA.chr20.bw Desktop/PG2018
    • Start IGV
      • Select “Human hg19” in the upper left
      • In the File menu, select “Load from File” and select the HUES64_rep1.mRNA.chr20.bw file in Desktop/PG2018
      • Change “All” to “chr20”, clicking upper right “+” to zoom
      • Navigate to chr20:18486382-18543963
    • Submit screenshot to your TA
  3. Plot RNA-seq data in R ( preview )
    • Download assignment ( prepwork-jun.Rmd )
    • Save work as prepwork-jun-lastname.Rmd and email to your TA