Analysing chip- seq data using Galaxy

Transcription

1 Analysing chip- seq data using Galaxy PhD programme 2013 Stéphanie Le Gras

2 Overview Top menu Analyze your data Log in/out HISTORY PANEL keep track of each jobs that have been run Grey: job is waikng to run Yellow: job is running Green: job is done Red: job encountered a problem TOOL PANEL Data display and tools dialog window Galaxy: hops://main.g2.bx.psu.edu/

3 BioinformaKcs workflow Sequences (reads) Assessing the quality of the data Mapping Peak deteckon VisualizaKon Clustering High Level analysis MoKf discovery AnnotaKon

4 LET S START ANALYZING

5 BioinformaKcs workflow Sequences (reads) Assessing the quality of the data Mapping Peak deteckon VisualizaKon Clustering High Level analysis MoKf discovery AnnotaKon

6 Fastq : Line : Tile : X : Y Read sequence Quality

7 Get data to be analyzed There are several ways of ge^ng the data uploaded into galaxy : Uploading directly the files you ve got on your computer Using the bp server included in Galaxy Using pre- loaded datasets

8 Get data to be analyzed - From your computer - 1. Select the right format: fastq 2. Browse and select the file 4. Validate 3. Select the right assembly (hg18) Galaxy: hops://main.g2.bx.psu.edu/

9 Get data to be analyzed - From your computer - Do the same for all files 1. Select the right format 2. Browse and select the file File is being processed Processing is done Galaxy: hops://main.g2.bx.psu.edu/ 4. Validate 3. Select the right assembly (hg18)

10 BioinformaKcs workflow Sequences (reads) Assessing the quality of the data Mapping Peak deteckon VisualizaKon Clustering High Level analysis MoKf discovery AnnotaKon

11 Assessing the quality of the data: FastQC NGS: QC and manipulakon - FastQC:Read QC reports using FastQC 1. The file to be analyzed: fastq file 2. Execute Look at the results Galaxy: hops://main.g2.bx.psu.edu/

12 Assessing the quality of the data: FastQC Galaxy: hops://main.g2.bx.psu.edu/

13 BioinformaKcs workflow Sequences (reads) Assessing the quality of the data Mapping Peak deteckon VisualizaKon Clustering High Level analysis MoKf discovery AnnotaKon

14 Aligning reads onto a reference genome: BowKe No file is proposed for analysis while there is a file that seems to be in the right format in the history 1. Galaxy: hops://main.g2.bx.psu.edu/

15 Aligning reads onto a reference genome: BowKe Problem : no file is proposed for analysis 1. Datatype 3. Save 2. Choose/enter fastqsolexa 4. Galaxy: hops://main.g2.bx.psu.edu/

16 Aligning reads onto a reference genome: BowKe 1. Select the right assembly 2. Select the file 3. Execute Galaxy: hops://main.g2.bx.psu.edu/

17 BioinformaKcs workflow Sequences (reads) Assessing the quality of the data Mapping Peak deteckon VisualizaKon Clustering High Level analysis MoKf discovery AnnotaKon

18 Visualizing the data: UCSC genome browser Galaxy: hops://main.g2.bx.psu.edu/

19 Visualizing the data: UCSC genome browser Your data AnnotaKon tracks UCSC: hop://genome.ucsc.edu/

20 Visualizing the data: UCSC genome browser UCSC: hop://genome.ucsc.edu/

21 Visualizing the data: UCSC genome browser Display mode: Change from dense to squish UCSC: hop://genome.ucsc.edu/

22 Visualizing the data: UCSC genome browser UCSC: hop://genome.ucsc.edu/

23 BioinformaKcs workflow Sequences (reads) Assessing the quality of the data Mapping Peak deteckon VisualizaKon Clustering High Level analysis MoKf discovery AnnotaKon

24 Peak calling : MACS 1. Select the treatment file: mig 2. Select the control file: ctrl 3. Tag size Galaxy: hops://main.g2.bx.psu.edu/ 4. Execute

25 Peak calling : MACS Galaxy: hops://main.g2.bx.psu.edu/

26 Peak calling : MACS Galaxy: hops://main.g2.bx.psu.edu/

27 Peak calling : MACS PosiKons of the peaks UCSC: hop://genome.ucsc.edu/

28 Peak calling : MACS Galaxy: hops://main.g2.bx.psu.edu/

29 Peak calling : MACS

30 Peak calling : MACS UCSC: hop://genome.ucsc.edu/

31 BioinformaKcs workflow Sequences (reads) Assessing the quality of the data Mapping Peak deteckon VisualizaKon Clustering High Level analysis MoKf discovery AnnotaKon

32 AnnotaKng peaks: GREAT UCSC: hop://genome.ucsc.edu/

33 AnnotaKng peaks: GREAT Get output UCSC: hop://genome.ucsc.edu/

34 AnnotaKng peaks: GREAT Get output UCSC: hop://genome.ucsc.edu/ Send query to GREAT

35 AnnotaKng peaks: GREAT GREAT: hop://bejerano.stanford.edu/great/public/html/

36 AnnotaKng peaks: GREAT GREAT: hop://bejerano.stanford.edu/great/public/html/