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Day 1: Linux/TACC Introduction and Raw Sequence structure
Part 1: Linux
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introduction
Part 2: Sequencing formats
Day 2: Raw Sequencing Quality Evaluation
Part 1: FASTQ manipulation tools
- 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
Day 2: Raw Sequencing Quality Evaluation
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- 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
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