/
Monday

Monday

Jul 30, 2015

BACK: 2015 Main Page

JOINME: https://join.me/bioinfosu

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)

Working with Unix (09:00-10:30)

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

Coffee Break 10:30-10:40 (10m)

Bioinformatics Applications and File Formats (10:40-12:00)

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)

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

Bioinformatic Applications File Formats Contd. (1:00-2:15)

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

RNA-seq Analysis (2:15-2:45)

  1. RNA-seq Reference-based and Genome-guided Assembly (Lecture): http://goo.gl/lIQ2oW

Coffee Break (2:45-3:00)

RNA-seq Analysis Contd. (3:00-5:00)

  1. RNA-seq Differential Expression Analysis (Hands-on): http://goo.gl/lVGplJ

Wrap-up 5:00-