HSLS MolBio Workshops

This hands-on workshop will teach how to (1) access a remote Unix machine (Center for Research Computing- HTC Cluster) using a text-based terminal, (2) use basic Unix commands for managing files and directories, and (3) access HTC Cluster-installed open-source bioinformatics software packages such as STAR, HISAT, GATK, and Kallisto.

You must sign up for a Center for Research Computing HPC allocation.

This workshop is based on the Software Carpentry Lesson on the Unix Shell.

Target Audience

Experimental biologists seeking to analyze next-generation sequencing data generated through experiments or retrieved from a repository such as GEO.

Powerpoints

• Power point - Presentation Slides
• Recorded Lecture Video (51 min)

Data Download

• Dataset - Practice dataset for students 
• Fastq file_onesample - Raw fastq file for practice
• Europian Nucleotide Archive 
• Unix cheat sheet 
• Vim (Text Editor) cheat sheet 

Software Registration

• Download and Install PUTTY
• Download and Install Filezilla Client for transferring files
• Request for Center for Research Computing Account (If you are a faculty or PI and don’t have an account in CRC, you can request a new user account and allocation.   If you are a student, postdoc, or staff, a faculty advisor or PI must request a user account for you )

Selected Tutorials

• Introducing the Shell
• Navigating Files and Directories
• Working With Files and Directories
• Pipes and Filters
• Loops
• Shell Scripts
• Finding Things 

Feedback

• Please evaluate this class

Support

• HSLS MolBio - for consultations