blank en berg pittsburgh 2011 ngs

8/3/2019 Blank en Berg Pittsburgh 2011 Ngs

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Using Galaxy for NGS Analysis
http://galaxyproject.org/http://galaxyproject.org/


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Overview


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Overview


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NGS Data


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A Note on FASTQ

Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQfi

le format for sequences with quality scores, and the

@UNIQUE_SEQ_ID

GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT

+

!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65


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Overview


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Available NGS Analysis

Toolsets,


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Prepare and Quality

Check

, , , , ,


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Combining Sequences and

Qualities


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Grooming --> Sanger


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Quality Statistics and

Box Plot Tool


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Read Trimming

Q li il i


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Quality Filtering


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Manipulate FASTQ


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Toolsets,


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Mapping NGS Data

, , , , , , , ,

, ,


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Mappers


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Toolsets,


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SNPs & INDELs


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Toolsets,


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Peak Calling / ChIP-seq

analysis

P t t Bi di


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Punctate Binding

Zhang et al.

Model-based

Analysis of ChIP-

Seq (MACS).

Genome Biol

(2008) vol. 9 (9)

pp. R137

, , ,


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MACS

,


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Diffuse Binding

Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq


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ChIP-seq Exercise
http://main.g2.bx.psu.edu/u/james/p/exercise-chip-seqhttp://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq


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I have Peaks, now

what?


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Genomic Interval Operations


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Secondary Analysis, ,

,

Concatenate the exons/introns and other files

Determine which Peaks overlap the region types (Join)

S d A l i


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Secondary Analysis


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Annotation Profiler

, , ,

, , , ,

,

A il bl NGS A l i


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Toolsets,


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RNA-seq


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TopHat

, , , , ,

C ffli k


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Cufflinks

,

Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly

C ff


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Cuffcompare


C ffdiff


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Cuffdiff

, ,


RNA T t i l


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RNA-seq Tutorial
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercisehttp://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise


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Overview


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Sample Tracking System

S i F ilit


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Sequencing Facility

Managers

}


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Sequencing Facility Users

,

C fi A il bl


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Configure Available

Request / Sample Options

,


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Configure the Sequencer


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Configure the Sequencer


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How does it all work?

Customer Creates a Request


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Customer Creates a Request

C t D ib


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Customer Describes

Request

Customer Adds a Sample


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Customer Adds a Sample

S l Add d S b it


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Samples Added, Submit

Request

S l t N t t


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Samples enter New state

S i F ilit i


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Sequencing Facility is

informed of Request

Sequencing Facility


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Sequencing Facility

Receives Samples


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Sequencing Finished

Extending Sample
http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/


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Extending Sample

Tracking with ngLims

Using Galaxy
http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/https://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglimshttps://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglimshttps://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglimshttps://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims


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Using Galaxy

Acknowledgments


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Acknowledgments
https://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeamhttps://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeamhttps://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeamhttps://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam


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http://galaxy.psu.edu/gcc2011


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,

,
http://galaxy.psu.edu/gcc2011http://galaxy.psu.edu/gcc2011

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