In this module, we will cover basic analysis methods for Next Generation Sequencing Data.
Overview of Next-generation sequencing technologies: data perspective
Principles behind SNP identification from resequencing data
Filtering and basic statistics on SNP genotyping data
Hands-on exercises and wrap-up
Learning contents (all at Module 2 google drive)
Day 6 (July 11)
Intro to *next generation sequencing (pdf)
Common operations with FASTA and FASTQ; FASTQ quality check and cleaning (slides)
Today's recap
Day 7 (July 12)
SNP calling methodology (slides)
CHEAT SHEET! Short cuts / tips (slides)
Datasets to use (gdrive)
Today's recap
Day 8 (July 13)
SNPs dataset post-processing
Datasets to use (gdrive)
Today's recap
Day 9 (July 14)
This is more a show and tell session that demonstrates the steps done for the following:
More genotyping data analyses (gdrive)
Exploring VCF data (bcftools, vcfutils, vcftools, R).
Basic stats, power filtering, and extracting data subsets (doc)
Today's recap
Day 10 (July 15)
Materials for today (gdrive)
PLINK files (format, conversion, extract region, filtering)
Command-line shell history
Using Crop Galaxy for filtering etc.
Crop Galaxy website
Today's recap