Lecture 11

Lecture 11

PDF Slides for Class Session 11

None this week

Hands-On for Class Session 11

• PDF version of Hands-on 11

Data sets for Class Session 11

• Saccharomyces cerevisiae GFF3 file

• Drosophila melanogaster, X-chromosome [GFF3 file] -- ftp://ftp.flybase.net/genomes/dmel/current/gff/dmel-X-r5.41.gff.gz

Readings and references

• Unix basics
  • Unix Tutorial for Beginners
• Software tools
  • Cygwin - Unix tools on Windows
• AWK tutorials
  • http://www.grymoire.com/Unix/Awk.html
  • http://www.vectorsite.net/tsawk.html
  • http://www.thegeekstuff.com/tag/awk-tutorial-examples/
• Bash tutorials
  • Bash programming, introduction
  • Advanced bash scripting
• Tutorials on grep and regular expressions
  • http://www.panix.com/~elflord/unix/grep.html
  • http://www.grymoire.com/Unix/Regular.html
• Specification of the GFF3 format
  • http://www.sequenceontology.org/gff3.shtml
• Posix character classes

Programming exercises

None this week

Assignments

None this week