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Table of Contents


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.


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


Sequencing background


References Dr. Loraine recommends

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




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