SummaryOld.md

A mountain of data is being generated each year and the this amount continues to grow at an exponential rate.

The Bioinformatics workbook is designed to very quickly gain experience on the most common bioinformatics problems.

Science today is seeing a transition from domain specific to interdisciplinary approaches of scientific inquiry.

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XSEDE

• test1
• Using PSC Supercell (storage for Bridges and Greenfield)
• Basics
• SLURM
  • SLURM: Submitting dependency jobs
  • SLURM: Job management cheat sheet
  • SLURM: generating job submission scripts for Condo
• Setting up BASH
  • Viewing files in remote machine without downloading locally
  • Guide for installing various types of programs in Linux
  • Introduction to Regular Expressions
  • Password-less SSH login
• PBS/Torque
  • PBS-Torque: Submitting dependency jobs
• Microsoft Excel related
  • Export multiple worksheets as separate text files in Excel
  • Import multiple text files as separate worksheets in Excel
  • Generate index sheet linking all spreadsheets in Excel
• File transfer
  • Downloading files via wget
  • Downloading SRA files from NCBI
  • File Transfer Using Globus Connect Personal (GCP)
  • Getting data from iPlant via iRODS
• NCBI tools
  • Running BLAST jobs in parallel
  • SRA
• FASTA/Q manipulations
  • Converting FASTQ format to FASTA
  • Bioawk Basics
  • FASTQ_quality_score_encoding
  • Retrieve FASTA sequences using sequence IDs
  • Calculate sequence lengths in a fasta file
  • Fastq quality trimming
  • Converting FASTQ to FASTA
• RNA-Seq
• DGE without a genome
  • Denovo Assembly
  • Counting reads
  • DGE
• DGE using a genome
  • Alignment
  • Counting reads
  • DGE
• Genome Assembly
• PacBio or MinION only
• Illumina only
• Genomescope
• Hybrid of short and long reads
• Comparative Genomics
• Reconstructing Species Phylogenetic tree with BUSCO genes using Maximum Likelihood method
• Metagenomics
• 16S
  • Qiime
  • Mothur
• Singularity and Containers
• Introduction
• Singularity
• Fastq quality trimming
• GO enrichment analysis