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Table of Contents

Introduction

By now, you've learned a great deal about how to work productively in a UNIX environment. You've also learned to perform one of the most fundamentally important tasks in bioinformatics programming, which is creating data sets for visualization by end user biologists.

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This week, you'll learn:

  • how to obtain get RNA-Seq data from the short-read archive
  • how to convert NCBI-specific sequence format (.sra) to FASTQ
  • how to interpret quality scores and other information in FASTQ files
  • how to align sequences in FASTQ files onto a reference genome
  • how to visualize files produced by alignment toolsalignments

References

Sequencing background

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References Dr. Loraine recommends

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

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samtools

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Aligning and visualizing RNA-Seq data. Due 5 pm, Thurs Sept, 27