galaxy rna-seq analysis: tuxedo protocol
DESCRIPTION
Galaxy RNA-Seq Analysis: Tuxedo ProtocolTRANSCRIPT
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Galaxy RNA-Seq Analysis: Tuxedo Protocol
ChangBum Hong, KT Bioinformatics, GenomeCloud SCIC genome-cloud.com
This work is licensed under the Creative Commons Attribution-NonCommercial- ShareAlike 3.0 New Zealand License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/nz/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.
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Introduction• RNA-Seq
• Transcriptome assembly
• Qualitative identification of expressed sequence
• Differential expression analysis
• Quantitative measurement of transcript expression
• RNA-Seq Applications
• Annotation: Identify novel genes, transcripts, exons, splicing events, ncRNAs
• Detecting RNA editing and SNPs
• Measurements: RNA quantification and differential gene expression
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Experimental design• What are my goals?
• Transcriptome assembly?
• Differential expression analysis?
• Identify rare transcripts?
• What are the characteristics of my system?
• Large, complex genome?
• Introns and high degree of alternative splicing?
• No reference genome or transcriptome?
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Splicing
AssemblyExpression
Differentially expressed
Experimental Outputs
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Sequencing• Platforms
• Library preparation
• Multiplexing
• Sequence reads
• File names
• Fastq format(Formats vary)
• 4 lines per readIllumina Read ID
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Data Quality Control
• Data Quality Assessment
• Identify poor/bad sample
• Identify contaminates
• Trimming: remove bad bases from read
• Filtering: remove bad reads from library
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Read Mapping• Alignment algorithm must be
• fast
• able to handle SNPs, indels, and sequencing errors
• allow for introns for reference genome alignment
• Input
• fastq read library
• reference genome index
• insert size mean and stddev(for paired-end libraries)
• Output
• SAM (text) / BAM (binary) alignment files
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Differential Expression
• Cuffdiff (Cufflinks package)
• Pairwise comparisons
• Differnetial gene, transcript, and primary transcript expression
• Easy to use, well documented
• Input: transcriptome, SAM/BAM read alignments
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Transcriptome Assembly• RNA-Seq
• Reference genome
• Reference transcriptome
• RNA-Seq
• Reference genome
• No reference transcriptome
• RNA-Seq
• No reference genome
• No reference transcriptome
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RNA
FASTQ
Reads
Experimental Design
Sequencing
Reference Genome
FASTA
Referecne Transcriptome
GFF/GTF
Data Quality Control
FASTQ
Tuxedo protocol
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Combining tools in a pipeline• Linux Command-line Tools
• Shell script, Makefile
• GUI Based pipeline
• DNANexus
• SevenBridegs Genomics
• Galaxy
• Open Source
• Wrapper for command line utilites
• Workflows
• Save all steps you did in your analysis
• Return the entire analysis on a new dataset
• Share your workflow with other people
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How to use Galaxy?
NO WAIT TIMES
NO STORAGE QUOTAS
NO JOB
SUBMISSION LIMITS
NO DATA
TRANSFER BOTTLENECKS
NO IT
EXPERIENCE REQUIRED
NO REQUIRED
INFRASTRUCTURECOST
GALAXY MAIN Free
LOCAL GALAXY Free ?
CLOUD GALAXY
(AMAZON)
동일사양 대비 약 2배 (KT의)
SLIPSTREAM GALAXY
$19,995 (2천2백만원)
KT GenomeCloud
GALAXY
시간당 740원부터
GALAXY MAIN: User disk quotas 250GB for registered users, maximum concurrent jobs: 8
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Outline of tutorial
• Starting Galaxy
• Mapping with Tophat
• Workflows
• Visualizing alignment with IGV
• Computing differential expression with cuffdiff
• Cuffdiff visuaalization with CummeRbund
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Starting Galaxy
• Tutorial Dataset
• Accessing Galaxy
• Import files for one sample into current history
• Set file attributes
• Run FastQC
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Tutorial Dataset• FASTQ files (fastq): Sequence Reads
• Reference (fasta): Genome Sequence (galaxy default)
• Geneset (GTF / GFF3): Reference Geneset
• Bowtie2 index: Reference index files for Bowtie2 (galaxy default)
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Tutorial Dataset Reference & Gene sets
• Ensembl
• http://www.ensembl.org/info/data/ftp/index.html
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Tutorial Dataset Reference & Gene sets
•illumina iGenomes • The iGenomes are a collection of reference sequences and annotation files for commonly analyzed
organisms. The files have been downloaded from Ensembl, NCBI, or UCSC, and chromosome names have been changed to be simple and consistent with their download source. Each iGenome is available as a compressed file that contains sequences and annotation files for a single genomic build of an organism.
• http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn
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Tutorial Dataset Sequencing data
•Sequencing data (Drosophila melanogaster) • Gene Expression Omnibus at accession GSE32038
• http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32038
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Biological replicates vs. technical replicates
Biological Replicates
Technical Replicates
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Accessing Galaxy• Open a web browser and navigate to Galaxy website usegalaxy.org or www.genome-cloud.com
• Log in with username and password
GenomeCloud (genome-cloud.com)
select galaxy service
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Tools pane
Center pane
History pane
when your galaxy is ready you will recive the e-mail
access the galaxy via public ip address
you can register via user menu > register
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Import files• Open a web browser and navigate to Galaxy website usegalaxy.org or www.genome-cloud.com
• Log in with username and passwordexample fastq and gtf files are located in shared data > RNA-Seq with Drosophila melanogaster
import data into your history panel (read to analysis)
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Set file attributes• In the history pane click on the pencil icon
• Enter “fastqsanger” (It will takes time)
Sanger Phread+33 fastqsanger (cassava 1.8 ▲ ) Ilumina 1.3 Phread+64 fastqillunina (cassava 1.8 ▼) Solexa Solexa+64 fastqsolexa
Tophat options --solexa-quals: Use the Solexa scale for quality values in FASTQ files --solexa1.3-quals: Phred64/Illumina 1.3~1.5 !BWA options -l : The input is in the Illumina 1.3+ read format (quality equals ASCII-64) !GenomeCloud (g-Analysis)
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CASAVA 1.8.2 Quality Score (or Q-score)
Error probability
Quality Score Encoding
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Run FastQC• Load the FastQC tool from the tool pane
• Set the input file (repeat this step on the C1, C2 all piar files)
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When fastqc has finished running, click on the eye on the FastQC output file to display
wait running done error
Galaxy status
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Per base sequence quality
Per sequence quality score
Per base sequence content
illumina (in-house data)
IonTorrent (in-house data)
illumina (good dataset in FastQC homepage)
illumina (bad dataset in FastQC homepage)
illumina (in-house data)
IonTorrent (in-house data)
illumina (good dataset in FastQC homepage)
illumina (bad dataset in FastQC homepage)
illumina (in-house data)
IonTorrent (in-house data)
illumina (good dataset in FastQC homepage)
illumina (bad dataset in FastQC homepage)
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Per base GC content
Per sequence GC content
Per base N content
illumina (in-house data)
IonTorrent (in-house data)
illumina (good dataset in FastQC homepage)
illumina (bad dataset in FastQC homepage)
illumina (in-house data)
IonTorrent (in-house data)
illumina (good dataset in FastQC homepage)
illumina (bad dataset in FastQC homepage)
illumina (in-house data)
IonTorrent (in-house data)
illumina (good dataset in FastQC homepage)
illumina (bad dataset in FastQC homepage)
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Sequence Length Distribution
Sequence Duplication Levels
illumina (in-house data)
IonTorrent (in-house data)
illumina (good dataset in FastQC homepage)
illumina (bad dataset in FastQC homepage)
illumina (in-house data)
IonTorrent (in-house data)
illumina (good dataset in FastQC homepage)
illumina (bad dataset in FastQC homepage)
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Mapping with Tophat
• Initial Tophat run
• Determine insert size
• Rerun Tophat with correct insert size
• Review mapping statistics
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Initial Tophat run• Use Full Tophat paramters
• Paired-end FASTQ files, Select reference genome, Use Own Juctions(Yes), Use Gene Annotation Model(Yes)
• Gene Model Anntations (use GFF file)
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Determine insert size• Load the insert size tool “NGS: Picard (beta) -> Insertion size meterics”
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Determine insert size• Click “eye” icon
• Identify the MIN_INSERT_SIZE (198)
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Rerun Tophat• Click any one of the Tophat2 output files in the history panne
• Click on the circular blue arrow icon
• Change the “Mean Inner Distance between Mate Pairs” (198)
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Tophat Output• unmapped.bam (BAM)
• accepted_hits.bam (BAM): a list of read alignments in BAM/SAM format
• junctions.bed (BED): list BED track of junctions reported by Tophat where each junction consists of two connected BED blocks where each block is as long as the max overhang of nay read spanning juction
• deletions.bed (BED): mentions the last genomic base before the deletion
• insertions.bed (BED): mentions the first genomic base of deletion
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Load files into IGV• Click on the “accepted hits” file in the history pane
• Click on the “display with IGV web current”
• A file named “igv.jnlp” will be downloaded by your browser
• Open with text editor copy BAM file location
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http://www.sabiosciences.com/rt_pcr_product/HTML/PADM-000Z.html
IGV with Housekeeping gene
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Load files into IGV• Enter “Act42A” in the search box to view the reads aligning
• Right-click on the coverage track and select “Set Data Range” (max value to 4372)
Housekeeping gene: Act42A
Set max value
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IGV with Differential Expression
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Keyword: regucalcin (calcium-binding protein)
this gene has four isoforms
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Load files into Trackster• Click on the “accepted hits” file in the history pane
• Click on the graph icon and select “Trackster”
• Select bam files
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create new group ‘Add group’drag into new group
move to regucalcin gene
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set max value
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Run cuffdiff• Load the Cuffdiff tool: “NGS:RNA Analysis->Cuffdiff ”
• Perform replicate analysis(Yes)
• Add new Group / Add new Replicate
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Cuffdiff output• Genes: gene differential FPKM
• Isoforms: Transcript differential FPKM
• CDS: Coding sequence differential FPKM
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View and filter cuffdiff output
• Differential Gene Expression (DGE)
• Filter out genes with significant change in expression with a log fold-change of at least 1 “C14 == ‘yes’ and abs(c10)>1” in the “With following condition” text box
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Cuffdiff visualization with CummeRbund
• Load the CummeRbund tool: NGS:RNA Analysis->cummerbund
• Plot type: Density, check the “Replicates” box
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Samples have similar density distribution(density plot)
Samples cluster by expression condition (MDS / PCA plot)
Samples cluster by experimental condition (Dendogram)
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Volcano Differential analysis results for regucalcin Expression plot shows clear differences in the expression of regucalcin across conditions C1
and C2 (four alternative isoforms)
Scatter plots highlight general similarities and specific outliers between conditions
C1 and C2
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Extract workflow from current history
• Click on the small gear icon and select “Extract Workflow”
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Edit workflow• Click on “Workflow” at the top of the Galaxy window
• Move the elements of the workflow
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Run workflow• Load a workflow by clicking on “Workflow” ath the top of the screen
• Click on “Run”
• Select the input datas
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• Public main galaxy site (user disk quotas 250GB for registered users, maximum concurrent jobs: 8)
• https://usegalaxy.org/
• Test galaxy site (beta site for galaxy main instance)
• https://test.galaxyproject.org/
• Galaxy screen cast and tutorials
• https://wiki.galaxyproject.org/Learn
• Galaxy를 이용한 NGS 분석 (Korean)
• http://hongiiv.tistory.com/701
• Galaxy를 이용한 SNP 분석 (Korean)
• http://hongiiv.tistory.com/652
• Galaxy를 이용한 부시맨 genome 분석 (Korean)
• http://hongiiv.tistory.com/655
Useful galaxy sites
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Thank you
Acknowledgements:YoungGi Kim HanKyu Choi
WanPyo Hong KangJung Kim