Barrick Lab :: Computational Protocols

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---+!! Barrick Lab :: Computational Protocols

---++ Command line
   * [[ProtocolsUnixCommandsQuickReference][Unix Commands Quick Reference]] <br>Collection of useful Unix commands.
   * [[ProtocolsSSHPublicKeyAuthentication][SSH Public Key Authentication]] <br> How to set up login without typing password between Linux machines.
   * [[ProtocolsMassRename][Rename files via command line]] <br>How to use sed to rename multiple files in a single directory.
   * [[AllowDisconnection][Leave a command running on a remote machine after logging out]] <br>How to start a command in a ssh session, and leave it running after logging out of the current window.
   * [[UnzipAll][Mass File Extraction]] <br>Simple script for 'un-tar'ing and 'un-zip'ing all .tar.gz files in a single directory

---++ Next generation sequencing data analysis
   * [[ProtocolsDcampCloning][Cloning DCAMP repository]] <br>Instructions for DCAMP repository, and getting permissions to push back to the repository.
   * [[ProtocolsSequenceRetrieval][GSAF Sequence Retrieval and Backup]] <br>Instructions for downloading and backing up data sent by UT GSAF.
   * [[ProtocolsIbcAssignment][Sample splitting using IBCs]] <br>Instructions for splitting pooled samples into individual samples based on internal barcodes.
   * [[ProtocolsGdGenerationl][Generate Genome Diff (.gd) Files From .fastq Files]] <br>Instructions for generating .gd files from .fastq files.
   * [[ProtocolsFlexbarCommands][Flexbar Commands for Trimming Adapter Sequences]] <br>Command line tools for trimming adapter sequence from NGS reads.
   * [[ProtocolsRunningBreseqOnTACC][Running <i>breseq</i> on TACC]]
   * [[ProtocolsRNASeqDifferentialExpression][Analyzing RNA-Seq data]] <br>Analyzing RNA-Seq data for differential expression.

---++ Data Management
   * [[PubliclyArchivingData][Publicly Archiving Data]]<br>Uploading data and obtaining an accession number from GenBank, SRA, and Dryad databases.

---++ BEACON
   * [[BEACONTeleconferenceSetup][How to set up the BEACON teleconference in GDC7.808]]

---++ Python
   * [[Regular Expressions][How to use regular expressions to parse through input files using Python.]]
This topic: Lab > WebLeftBar > ComputationList
Topic revision: r10 - 2016-05-31 - DanielDeatherage