defense of my bsc-thesis
DESCRIPTION
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-jedenTRANSCRIPT
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
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
• cheap to produce
• fast way of producing data
• allows comparative analysis
Assembly
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
Assembly
read 1
read III
read 1V read 1I
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
Assembly
read 1 read III
read 1Vread 1I
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
Assembly
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation
Assembly
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
Annotation
Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
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
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
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
How is it done?What tools do exist?
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
How is it done?
What tools do exist?
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
How is it done?What tools do exist?Assembly
SNP-Detection
Homology-Detection
ORF-Prediciton
CAP3 QualitySNP BLAST ESTScan
MIRA AutoSNP FASTX/FASTY ORFPredictor
PolyBayes HMMER
MIRA PatternHunter
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
Toolword count
of the manual
BLAST2GO 618
BLAST 3469
HMMER 32213
MIRA 71654
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
Chin et al, 1998
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
Beyond the CLIGetting around the Drawbacks
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Chin et al, 1998
• minimize choice of tools
• minimize the parameters for each tool
• add a graphical user interface
PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Task Tool
File-ConversionPerl- & Python-
Scripts
Assembly MIRA
SNP-Detection MIRA
Homology-Detection
BLAST
ORF-Prediction ORFPredictor
Pfam-Annotationpfam_scan /
HMMER
GO-Annotation BLAST2GO
PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Task Tool
File-ConversionPerl- & Python-
Scripts
Assembly MIRA
SNP-Detection MIRA
Homology-Detection
BLAST
ORF-Prediction ORFPredictor
Pfam-Annotationpfam_scan /
HMMER
GO-Annotation BLAST2GO
PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Task Tool
File-ConversionPerl- & Python-
Scripts
Assembly MIRA
SNP-Detection MIRA
Homology-Detection
BLAST
ORF-Prediction ORFPredictor
Pfam-Annotationpfam_scan /
HMMER
GO-Annotation BLAST2GO
PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Task Tool
File-ConversionPerl- & Python-
Scripts
Assembly MIRA
SNP-Detection MIRA
Homology-Detection
BLAST
ORF-Prediction ORFPredictor
Pfam-Annotationpfam_scan /
HMMER
GO-Annotation BLAST2GO
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Distributed Ruby
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Distributed Ruby
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby
Results
Zostera marina
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Image: Colin Faulkingham, CC-BY-SA 2.5
Results
Zostera marina
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Image: Colin Faulkingham, CC-BY-SA 2.5
866838 454-reads
Results
Zostera marina
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Image: Colin Faulkingham, CC-BY-SA 2.5
866838 454-reads
35364 contigs
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
Shortcomings
• only basic analysis due to lack of parameters of single tools
• no graphical representation of results
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
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary
Solutions• add optional “expert” parameters
• implement graphical representations
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
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
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)