Beyond the Command-
    Line Interface:
Transcriptome Analysis based on Next-Generation-
                Sequencing Data
Beyond the Command-
    Line Interface:
Transcriptome Analysis based on Next-Generation-
                Sequencing Data
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                 T...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                  ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                  ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                  ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                  ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                  ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                  ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                  ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                  ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




         ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




         ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




         ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




         ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




         ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Rub...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results



                ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results



                ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results



                ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary



      ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary



      ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary




     ...
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary




     ...
it´s your turn: feel free
    to ask questions




              image: Joe Rosenthal & Shigeru Miyamoto (fair use)
it´s your turn: feel free
    to ask questions




              image: Joe Rosenthal & Shigeru Miyamoto (fair use)
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Defense of my BSc-Thesis

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The slides i used for the defense of my BSc-Thesis. A blogpost in german about the work can be found here: http://www.wissenslogs.de/wblogs/blog/bierologie/biologie/2010-08-11/meine-bachelor-arbeit-transkriptom-analysen-f-r-jeden

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Defense of my BSc-Thesis

  1. 1. Beyond the Command- Line Interface: Transcriptome Analysis based on Next-Generation- Sequencing Data
  2. 2. Beyond the Command- Line Interface: Transcriptome Analysis based on Next-Generation- Sequencing Data
  3. 3. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Transcriptome Analysis • cheap to produce • fast way of producing data • allows comparative analysis
  4. 4. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly
  5. 5. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly read III read 1 1V read 1I re ad
  6. 6. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly read 1I read 1V read 1 read III
  7. 7. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly
  8. 8. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly
  9. 9. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Annotation Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
  10. 10. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Annotation Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
  11. 11. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Annotation Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
  12. 12. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks What tools do exist? How is it done?
  13. 13. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks How is it done? What tools do exist?
  14. 14. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks What tools do exist? How is it done? SNP- Homology- ORF- Assembly Detection Detection Prediciton CAP3 QualitySNP BLAST ESTScan MIRA AutoSNP FASTX/FASTY ORFPredictor PolyBayes HMMER MIRA PatternHunter
  15. 15. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks
  16. 16. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks word count Tool of the manual BLAST2GO 618 BLAST 3469 HMMER 32213 MIRA 71654
  17. 17. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks Drawbacks • spoilt for choice by the amount of tools • time-consuming to find right tools • lots of parameters to learn • the command-line interface is unintuitive Chin et al, 1998
  18. 18. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Beyond the CLI Getting around the Drawbacks • minimize choice of tools • minimize the parameters for each tool • add a graphical user interface Chin et al, 1998
  19. 19. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline
  20. 20. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline Task Tool Perl- & Python- File-Conversion Scripts Assembly MIRA SNP-Detection MIRA Homology- BLAST Detection ORF-Prediction ORFPredictor pfam_scan / Pfam-Annotation HMMER GO-Annotation BLAST2GO
  21. 21. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline Task Tool Perl- & Python- File-Conversion Scripts Assembly MIRA SNP-Detection MIRA Homology- BLAST Detection ORF-Prediction ORFPredictor pfam_scan / Pfam-Annotation HMMER GO-Annotation BLAST2GO
  22. 22. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline Task Tool Perl- & Python- File-Conversion Scripts Assembly MIRA SNP-Detection MIRA Homology- BLAST Detection ORF-Prediction ORFPredictor pfam_scan / Pfam-Annotation HMMER GO-Annotation BLAST2GO
  23. 23. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline Task Tool Perl- & Python- File-Conversion Scripts Assembly MIRA SNP-Detection MIRA Homology- BLAST Detection ORF-Prediction ORFPredictor pfam_scan / Pfam-Annotation HMMER GO-Annotation BLAST2GO
  24. 24. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  25. 25. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  26. 26. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  27. 27. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  28. 28. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  29. 29. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  30. 30. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  31. 31. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  32. 32. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  33. 33. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  34. 34. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Distributed Ruby
  35. 35. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Distributed Ruby
  36. 36. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results Results Zostera marina Image: Colin Faulkingham, CC-BY-SA 2.5
  37. 37. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results Results Zostera marina 866838 454-reads Image: Colin Faulkingham, CC-BY-SA 2.5
  38. 38. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results Results Zostera marina 866838 454-reads 35364 contigs Image: Colin Faulkingham, CC-BY-SA 2.5
  39. 39. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results
  40. 40. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results
  41. 41. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results
  42. 42. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results
  43. 43. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Shortcomings & Solutions / Summary Shortcomings • only basic analysis due to lack of parameters of single tools • no graphical representation of results
  44. 44. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Shortcomings & Solutions / Summary Shortcomings • only basic analysis due to lack of parameters of single tools • no graphical representation of results Solutions • add optional “expert” parameters • implement graphical representations
  45. 45. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Shortcomings & Solutions / Summary Summary • Transcriptome Analysis needs software tools • Many different tools for each task exist • Most of them are CLI-driven • People don‘t like the CLI
  46. 46. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Shortcomings & Solutions / Summary Summary • Built a pipeline that provides usual tools and a GUI • The pipeline works for standard tasks of Transcriptome Analysis • In an upcoming version more tool- parameters & graphical results shall be added
  47. 47. it´s your turn: feel free to ask questions image: Joe Rosenthal & Shigeru Miyamoto (fair use)
  48. 48. it´s your turn: feel free to ask questions image: Joe Rosenthal & Shigeru Miyamoto (fair use)
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