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Add hands-on sections #8

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rkhetani opened this issue Jul 5, 2018 · 0 comments
Open
10 tasks

Add hands-on sections #8

rkhetani opened this issue Jul 5, 2018 · 0 comments

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@rkhetani
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rkhetani commented Jul 5, 2018 •
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Before and/or during raw data QC lesson

  • Logging in to the cluster
  • Starting an interactive session
  • Few basic commands: mkdir, cd, ls -l, tree
  • introduction to modules
  • run fastqc
  • run fastqc using a slurm script on all 6 files
  • use filezilla to copy over fastqc result

After DE analysis, but before the R-based data visualization

  • Introduction to IGV and looking at 2 or 3 top DE genes

Before Functional analysis, could be part of visualization

  • basic introduction to RStudio panels
  • open a prewritten script and run lines/chunks of code to wrangle tables and draw a volcano plot or heatmap
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@rkhetani