Martijn Masoed Nick Rico

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Presentation transcript:

Martijn Masoed Nick Rico http://www.google.nl/search?hl=nl&site=imghp&tbm=isch&source=hp&biw=1317&bih=736&q=lotus+toiletpapier&oq=lotus+toi&gs_l=img.3.0.0j0i24l8.1277.2803.0.3941.9.8.0.1.1.0.170.824.4j4.8.0...0.0...1ac.1.4.img.jqy4uSel18g#imgrc=UDAeYp50u-9qyM%3A%3B-QHscySXjk2-qM%3Bhttp%253A%252F%252Fwww.aquatube.eu%252Fmedia%252F6920%252Fdemo_benl.jpg%3Bhttp%253A%252F%252Fwww.aquatube.eu%252Fnl%252Fhome.aspx%3B335%3B187 Martijn Masoed Nick Rico

Index Dataset TopHat, Cufflinks (1) Cuffmerge, Cuffdiff, analyse (2)

Dataset Arabidopsis thaliana (advanced) Six conditions: Cold stress Drought stress Heat stress Highlight stress Salt stress Control

Pipeline (1) Input data (FastQ) Tophat Bamfile Cufflinks Transcripts.gtf

Biological interpretation Pipeline (2) Control vs condition transcript.gtf Cuffmerge Merged.gtf Bamfile Cuffdiff DE-genes Get_functions Biological interpretation

Time schedule Day 1 2 3 4 5 Task Make a planning. Run tophat + cufflinks Run cuffmerge + cuffdiff Bio interpretation + GO analysis. Planning presentation Moduel of co-expressed genes. Advanced tasks Check R (WGCMA) Evt. Conserved modules. Day 6 7 8 9 10 Task Report Wrap up project tasks Wrap up project tasks Report + presentation Report + Presentation Presentation

Questions http://www.google.nl/search?hl=nl&site=imghp&tbm=isch&source=hp&biw=1317&bih=736&q=lotus+toiletpapier&oq=lotus+toi&gs_l=img.3.0.0j0i24l8.1277.2803.0.3941.9.8.0.1.1.0.170.824.4j4.8.0...0.0...1ac.1.4.img.jqy4uSel18g#hl=nl&site=imghp&tbm=isch&sa=1&q=question+mark+dna&oq=question+mark+dna&gs_l=img.3...15367.15759.2.15955.3.3.0.0.0.0.105.255.2j1.3.0...0.0...1c.1.4.img.gBKlgQdy5Lw&bav=on.2,or.r_gc.r_pw.r_qf.&fp=fa6cba94002e5b1d&biw=1317&bih=736&imgrc=639pWDoVypRzpM%3A%3B5kEJk9HSaxZUFM%3Bhttp%253A%252F%252Fprojects.nfstc.org%252Fotc%252Fimages%252Fmodule1%252FDNACD_mod01-1-04.jpg%3Bhttp%253A%252F%252Fprojects.nfstc.org%252Fotc%252Fmodule1%252F1.1.004.htm%3B185%3B300