Schumer lab:Github and bioinformatics wiki

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

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

Useful bioinformatics resources

• Useful web programs
• slurm resources

Data map on Oak

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