<noautolink> <!-- Preferences start here * Set PAGETITLE = Barrick Lab :: Computational Protocols Preferences end here --> ---+!! Barrick Lab :: Computational Protocols ---++ Getting Started * [[ProtocolsLearnBiocomputing][Learn Biocomputing]] %BR% Resources for learning the command line, R, Python, GitHub, etc. * [[ProtocolsPythonSnippets][Useful Python snippets for biology]] %BR% Short code blocks for preforming common tasks in Python ---++ 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. * [[CommandLineBox][Command Line File Transfer to UT Box]] <br />How to directly transfer files to/from TACC or other computers to UT Box using LFTP. * [[WorkingWithGit][Working with Git(Hub)]] <br /> Links for learning Git and commonly used workflows/commands. ---++ 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. * [[ProtocolsTrimmomaticCommands][Trimmomatic Commands for Trimming Adapter Sequences]] <br />Command line tools for trimming adapter sequence from NGS reads (current method). * [[ProtocolsFlexbarCommands][Flexbar Commands for Trimming Adapter Sequences]] <br />Command line tools for trimming adapter sequence from NGS reads (deprecated method). * [[ProtocolsRunningBreseqOnTACC][Running _breseq_ on TACC]] * [[ProtocolsRNASeqDifferentialExpression][Analyzing RNA-Seq data]] <br />Analyzing RNA-Seq data for differential expression. ---++ Bacterial Gene/Genome Analysis * Predicting transcription start sites: [[http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb][BPROM]] | [[http://bioinformatics.biol.rug.nl/websoftware/ppp/ppp_start.php][PPP]] | [[http://www.fruitfly.org/seq_tools/promoter.html][NNPP]] ---++ Data Management * [[PubliclyArchivingData][Publicly Archiving Data]]<br />Uploading data and obtaining an accession number from GenBank, SRA, and Dryad databases. ---++ R * [[UsefulRTools][Useful R packages for manipulating and presenting data.]] * [[RAnimation][Creating animations for visualizing time resolved data.]]
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Topic revision: r26 - 2020-12-17 - JeffreyBarrick