Defense of my BSc-Thesis

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 Transcriptome Analysis • cheap to produce • fast way of producing data • allows comparative analysis

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 read III read 1 1V read 1I re ad

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly read 1I read 1V read 1 read III

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 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 What tools do exist? How is it done?

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 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

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 word count Tool 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 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

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

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline

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

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 Zostera marina / Results Results Zostera marina Image: Colin Faulkingham, CC-BY-SA 2.5

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

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

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 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 Solutions • add optional “expert” parameters • implement graphical representations

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

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

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

Defense of my BSc-Thesis

by Bastian Greshake on Aug 24, 2010

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Defense of my BSc-Thesis — Presentation Transcript