Page History

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Day 2: Raw Sequencing data manipulation

• Evaluating raw sequencing data
  • Overview of NGS data formats and analyses
  • The FASTA sequencing data format
  • The FASTQ sequencing data format, with Illumina/GSAF-specific details
  • Compression, Linux manipulation of fastq files
  • Overview of sequence quality checking
  Evaluating raw sequencing data
  • FASTQC - a good place to start
  • FASTX toolkit manipulation of FASTQ data
  • Adapter trimming with cutadapt
  • Batch manipulation of FASTQ files
• Overview of read alignment, references and alignment tools

Day 3: Alignment and BAM file manipulation

Part 1: Alignment and aligners

• Overview of read alignment, references and alignment tools
• BWA overview, relevant options
• Bowtie2 overview, relevant options
• Visualizing alignments with the Integrative Genomics Viewer (IGV)

Part 2: SAM/BAM format and manipulation

• The SAM file format specification
• Manipulating BAM files with samtools
• Alignment filtering examples

Day 4: Post-Alignment

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Analysis

Part 1: Bedtools

• Analysis with bedtools

Part 1:

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Odds and

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ends

• Data formats for visualization (BED, GTF/GFF)
• The Integrative Genomics Viewer (IGV)
• UCSC Genome Browser

Part 2: SAM/BAM format and manipulation

Enrichment modules

• Analysis with bedtools
• Obtaining public datasets from NCBI
• Core NGS Tools -- Resources

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• Obtaining public datasets from NCBI
• Shell scripting

Link to Etherpad: https://etherpad.mozilla.org/g2NxIEAFWL

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