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
1. Beyond the Command-
Line Interface:
Transcriptome Analysis based on Next-Generation-
Sequencing Data
2. Beyond the Command-
Line Interface:
Transcriptome Analysis based on Next-Generation-
Sequencing Data
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. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
Assembly
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. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
Assembly
read 1I read 1V
read 1 read III
7. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
Assembly
8. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
Assembly
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. 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. 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. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
What tools do exist?
How is it done?
13. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
How is it done?
What tools do exist?
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. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
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. 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. 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. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Pipeline
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. 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. 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. 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. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
25. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
26. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
27. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
28. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
29. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
30. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
31. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
32. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
33. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
34. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Distributed Ruby
35. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Distributed Ruby
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. 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. 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. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
40. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
41. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
42. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
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. 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. 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. 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. it´s your turn: feel free
to ask questions
image: Joe Rosenthal & Shigeru Miyamoto (fair use)
48. it´s your turn: feel free
to ask questions
image: Joe Rosenthal & Shigeru Miyamoto (fair use)