Schumer lab:Github and bioinformatics wiki

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Make sure to flag pipelines/scripts that aren't working properly under the Lab Meeting channel on slack

Please remember to add scripts that you have thoroughly tested to the lab GitHub and document here

Contents

  • 1 Bioinformatics topics
  • 2 Where to find important files and resources?
  • 3 Data map on Oak
  • 4 Useful bioinformatics resources

Bioinformatics topics

  • Introduction to command line
  • Common file formats
  • Commonly used scripts
  • Commonly used programs
  • Commonly used workflows
  • Important simulation tools
  • Submitting slurm jobs
  • Lab group on Sherlock
  • Where can I find commonly used files?
  • Useful Unix/perl/awk commands
  • Lab github
  • Common errors
  • Download data to Sherlock from Admera
  • Download data to sherlock from box, dropbox or googledocs
  • Download data to Sherlock from NCBI's SRA
  • Upload data from Sherlock to NCBI's SRA
  • Sharing data with collaborators

Where to find important files and resources?

  • Shared resources
  • Swordtail Dropbox quick guide

Data map on Oak

  • Depositing data on Oak
  • Data currently available on Oak
  • Processed files available on Oak
  • Backing up raw data
  • Lab member folders

Useful bioinformatics resources

  • Useful web programs
  • slurm resources
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Schumer_lab:Github_and_bioinformatics_wiki&oldid=1111113"

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  • This page was last edited on 23 May 2023, at 15:15.
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