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.
R
Useful R packages for manipulating and presenting data.
Creating animations for visualizing time resolved data.
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ComputationList
Contributors to this topic
JeffreyBarrick, DanielDeatherage, SimonDAlton, JuliePerreau, LucyLeblanc, StellaWang, MattMcGuffie
Topic revision: r26 - 2020-12-17 - 13:34:22 - Main.JeffreyBarrick
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