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Approches génomiques – TP 4 L3 – BCP Méthodes Moléculaire en Ecologie de Microorganismes

Approches génomiques – TP 4 L3 – BCP Méthodes Moléculaire en Ecologie de Microorganismes . Lois Maignien MCf IUEM lois.maignien@univ-brest.fr. Enseignant. Loïs Maignien MCf EcoGenomique Lois.maignien@univ-brest.fr 0290915380 – IUEM Salle A223 Ecologie microbienne Bioinformatique

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Approches génomiques – TP 4 L3 – BCP Méthodes Moléculaire en Ecologie de Microorganismes

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  1. Approches génomiques – TP 4L3 – BCP Méthodes Moléculaire en Ecologie de Microorganismes Lois MaignienMCf IUEM lois.maignien@univ-brest.fr

  2. Enseignant Loïs MaignienMCfEcoGenomique Lois.maignien@univ-brest.fr 0290915380 – IUEM Salle A223 • Ecologie microbienne • Bioinformatique • Ecologie moléculaire

  3. Galaxy • Galaxy permet de manipuler des jeux de données NGS a partir d’une interface web. Les lignes de commandes et les programmes on été transformés en formulaire web. • Permet de créer facilement des worflow: les in/out sont standardisés et le jeu de sortied’une opération devient le jeu d’entrée de la suivante.

  4. Tutoriel Galaxy • Exercice: quel est l’exon qui possede le plus de snp sur le chromosome 6 humain? Combien de variant? Combien d’exons ont plus de 20 snp? • Tutoriel classique de galaxy. Autre version: http://bsc2010.bioinformatics.ucdavis.edu/wp-content/uploads/2010/10/Joshi-Nik-HANDSON-Galaxy.pdf

  5. Etape 1. login sur l’instance de la station biologique Roscoff • http://abims.sb-roscoff.fr/faq. • Login: stageX X=04; 05; 06;…23;24. • Pw: stage,Y Y=4; 5; 6… 23; 24.

  6. Etape 2: selectionner les exons du chr6 • In the Tools pane, click on the Get Data menu and select one of the UCSC Table Browser options (UCSC Main or UCSC Inhouse for our UCDavis UCSC Table Browser data) • Once the UCSC Table Browser view is in the middle pane, the defaults should be A. Clade: Vertebrate, B. Genome: Human, C. Assembly: Mar 2006, D. Group: Genes and Gene Prediction Tracks, E. Track: UCSC Genes, F. Table: knownGene. For the G. region, let’s query chr6:1-25000000 and make sure the H. Output Format is set to BED- Browser Extensible Data. Make sure I.Send output to Galaxy is selected and press the J. get output button near the bottom of the page. • On the next page, click the button for A. Coding Exons and click the B. Send Query to Galaxy button.

  7. Etape 2: selectionner les exons du chr6

  8. Etape 3: sélectionner les SNP du chr6 • Again, click on the Get Data menu and select one of table browser options (main or inhouse). • Once the UCSC Table Browser view is in the middle pane, use the following menu options A. Clade: Vertebrate, B. Genome: Human, C. Assembly: Mar 2006, D. Group: Variation and Repeats, E. Track: SNPs(130), F. Table: snp130. For the G. region, let’s query the same region, chr6:1-25000000. Again, make sure the H. Output Format is set to BED and I. send output to Galaxy is checked. Then, click on the J. get output button. Use the default options on the next page and click on the Send Query to Galaxy button.

  9. Etape 3: sélectionner les SNP du chr6

  10. Etape 3: sélectionner les SNP du chr6 • So that we can better keep track of the data, let’s rename each data query in the History pane by clicking the A. pencil icon. I renamed my first query to B. Exons Hg18 chr6 and Snps Hg18 chr6 for the second query. Click on the save button after you have changed the name.

  11. Etape 5: visualiser et editer les jeux de donée

  12. Etape 5: Compter le nombre de SNP par exon du chr6 • In the tool | searchfield type « interval » Select • NGS: BedTools • Count intervals in one file overlapping intervals in another file Count number of interval in “SNPs Hg18 Chr6” in « Exons Hg18 Chr6 »

  13. Etape 5: Compter le nombre de SNP par exon du chr6

  14. Etape 6: filtrer les exons qui ont plus de 20 SNP • Filter and Sort • Filter data on any column using simple expressions Sort dataset ‘count of overlaps in Snps Hg18 chr6 on Exons Hg18 chr6’ • Visualize with “display at UCSC main”

  15. Etape 6: filtrer les exons qui ont plus de 20 SNP

  16. Etape 7: visualiser ces exons dans un navigateur de Genome • Visualize with “display at UCSC main”

  17. Etape 7: visualiser ces exons dans un navigateur de Genome

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