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2015 OSU Workshop: Monday

2015 OSU Workshop: Monday

Aug 03, 2015

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Opening Session (8:30-09:00)

  1. Overview of workshop. Present common resources (wiki, schedule, links) (10m)
  2. Instructor and participant round-robin intro (20m)

Introduction to OSU HPCC (09:00-09:30)

  1. OSU High Performance Computing Center: https://goo.gl/46c1iS

Working with Unix (09:30-11:00)

  1. Unix command-line basics (Lecture): http://goo.gl/KK2Y9q
  2. Working with the command-line (Hands-on): http://goo.gl/BcWMht

Coffee Break 11:00-11:15 (15m)

Sequencing technologies (11:15-12:00)

  1. Genome Sequencing Basics (Lecture): https://goo.gl/z0plK5
  2. Genome Sequencing Changing Science (Lecture): https://goo.gl/8G5ts1

Lunch Break 12:00-1:00 (60m)

Bioinformatics Applications and File Formats (1:00-2:30)

Lectures (http://goo.gl/QVhMiw) interspersed with 4 Hands-on sessions (http://goo.gl/3ufxLu)

  1. Sequence File Formats (and associated analysis tools)
    1. Module 1: FASTA (BLAST, MSA)
    2. Module 2: FASTQ (FastQC, Trimmomatic)

Coffee Break 2:30-2:45 (15m)

Bioinformatics Applications and File Formats (2:45-5:00)

  1. Genomic Interval File Formats
    1. Module 3: GFF3/BED (bedtools, Kent Tools)
  2. NGS File Formats
    1. Module 4: SAM/BAM (SAMTOOLS)

Wrap-up 5:00 -