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We will meet in Room 101B of the Flawn Academic Center (FAC) building. We STRONGLY encourage you to use the computers provided in the classroom, but you may also bring your personal laptops. |
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Day 1: Linux/TACC Introduction
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Day 2: Raw Sequencing
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data manipulation
- 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
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