Barrick Lab :: Computational Protocols

Getting Started

• Learn Biocomputing
  Resources for learning the command line, R, Python, GitHub, etc.
• Useful Python snippets for biology
  Short code blocks for preforming common tasks in Python

Command line

• Unix Commands Quick Reference
  Collection of useful Unix commands.
• SSH Public Key Authentication
  How to set up login without typing password between Linux machines.
• Rename files via command line
  How to use sed to rename multiple files in a single directory.
• Leave a command running on a remote machine after logging out
  How to start a command in a ssh session, and leave it running after logging out of the current window.
• Mass File Extraction
  Simple script for 'un-tar'ing and 'un-zip'ing all .tar.gz files in a single directory.
• Command Line File Transfer to UT Box
  How to directly transfer files to/from TACC or other computers to UT Box using LFTP.
• Working with Git(Hub)
  Links for learning Git and commonly used workflows/commands.

Next generation sequencing data analysis

• Cloning DCAMP repository
  Instructions for DCAMP repository, and getting permissions to push back to the repository.
• GSAF Sequence Retrieval and Backup
  Instructions for downloading and backing up data sent by UT GSAF.
• Sample splitting using IBCs
  Instructions for splitting pooled samples into individual samples based on internal barcodes.
• Generate Genome Diff (.gd) Files From .fastq Files
  Instructions for generating .gd files from .fastq files.
• Trimmomatic Commands for Trimming Adapter Sequences
  Command line tools for trimming adapter sequence from NGS reads (current method).
• Flexbar Commands for Trimming Adapter Sequences
  Command line tools for trimming adapter sequence from NGS reads (deprecated method).
• Running breseq on TACC
• Analyzing RNA-Seq data
  Analyzing RNA-Seq data for differential expression.

Bacterial Gene/Genome Analysis

• Predicting transcription start sites: BPROM | PPP | NNPP

Data Management

• Publicly Archiving Data
  Uploading data and obtaining an accession number from GenBank, SRA, and Dryad databases.

Data Analysis

• How to analyze Fluctuation Test data using rSalvador analysis package.

R

• Useful R packages for manipulating and presenting data.
• Creating animations for visualizing time resolved data.