Analysis Infrastructure for the ERC Consortium Sai Lakshmi Subramanian ERC Consortium Data Management amp Resource Repository DMRR Baylor College of Medicine Houston TX 5 th NIH ERCC Investigators Meeting ID: 655221
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exRNA Profiling Data Submission & Analysis Infrastructure for the ERC Consortium
Sai Lakshmi SubramanianERC Consortium Data Management & Resource Repository (DMRR)Baylor College of Medicine, Houston, TX
5
th
NIH ERCC Investigators’ Meeting
November 9
th
and 10
th
, 2015
Bethesda, MDSlide2
2Conflicts of Interest DisclosureI have no conflicts of interest to disclose.Slide3
3OverviewPoster Board 1Slide4
4Tools available at the DMRR exceRpt small RNA-seq Pipeline – Genboree Workbench & FTP Submission
RSEQtools long RNA-seq Pipeline – Genboree Workbench
Target Interaction Finder
– Genboree Workbench
Pathway Finder
– Genboree Workbench
Data Analysis Pipelines & Tools
exRNA FTP data submission pipeline for small RNA profiling data
Long RNA-seq data submission pipeline
Coming Soon
qPCR Assay data submission
Coming Soon
Data Submission Pipelines
Small RNA-Seq Assays
Long RNA-Seq AssaysqPCR Assays Coming Soon
exRNA Metadata Tracking -
GenboreeKBSlide5
Small exRNA-seq Data SubmissionSlide6
6exRNA Profiling Data Flow
Data Submission Pipeline
FTP submission of small exRNA-seq Data & Metadata
Data Analysis Pipelines
exceRpt small RNA-seq
exRNA Metadata Tracking System
GenboreeKB – small RNA-seq assays
Data
Metadata
Data Repository
exRNA Atlas
Pathway and Interaction Analysis
Target Interaction Finder
Pathway FinderSlide7
7exRNA AtlasView Tutorial Video at:http://genboree.org/theCommons/projects/exrna-mads/wiki/exRNA%20Atlas#Introduction-to-the-exRNA-AtlasSlide8
8exRNA AtlasFaceted search of submitted samplesSlide9
9Sample Subselection in exRNA AtlasSlide10
10Grids in exRNA AtlasSlide11
11Submission Summaries in AtlasSlide12
12Submission Summaries in AtlasSlide13
13Drill-down search in exRNA AtlasUse the circular partition diagram (or "sunburst" diagram) to interactively drill down into different subsets of biosamples.If you hover over a colored segment, you will see the Disease » Biofluid » Anatomical Location values for the biosamples in that subset.The
percentage of samples falling into that subset will also be displayed.If you click a specific segment, you will zoom into that subset.This drill-down tactic is the best approach for low-population subsets that are hard to select when zoomed out.
Clicking the
Search
icon in the floating
menubar
will open the tabular view of your biosample
subset.
Click the center circle to zoom out to the previous level.
Your last hovered path is always visible. To clear it, click outside the circle
.Slide14
14Drill-down search in exRNA AtlasSlide15
Genboree FTP Data Submission Pipeline15
Create an FTP account
Step 0
Prepare your data archive
Step 1
Prepare your metadata archive
Step 2
Prepare your manifest file
Step 3
Upload your submission to the FTP server
Step 4
D
ownload your results, perform pathway analysis
Step 5
Email DCC (
sailakss@bcm.edu
) for an account on the FTP server.
If you have exRNA profiling data
ftp.genboree.org
Use your Genboree user name and password
Genboree FTP Server
A dedicated, unique and private directory named
“
exrna-picode
”
for your lab/group, shared only by your lab members
and/or collaborators.
Upload directory
Slide16
Files to Submit
Contains your input data files
Data Archive File
FILE EXTENSION
- _
data.zip
or _
data.tar.gz
FORMAT
–
FASTQ/SRA format
(can be compressed)
REQUIRED
FILES - .fastq or .fastq.gz
or .fastq.zip or .sraOPTIONAL FILES – Spike in sequence file in FASTA format.
Contains metadata about your inputsMetadata Archive File
FILE
EXTENSION
- _
metadata.zip
or _
metadata.tar.gz
FORMAT
– All metadata files should be in
tab separated value format
REQUIRED
FILES
- .
metadata.tsv files - Submission, Study, Run, Experiment(s), Biosample(s) and Donor(s) documents.Contains details of your submission
Manifest file
FILE EXTENSION - .manifest.jsonFORMAT - JSON formatREQUIRED -
Genboree login name, group name, database name List all files that are submitted, MD5 checksumTool specific settingsAll three files must have the same basic file name: Example:samples_data.zipsamples_metadata.zipsamples.manifest.jsonSlide17
17exceRpt v3.1.9 WorkflowDeveloped by Rob Kitchen at the Gerstein Lab, Yale UniversitySlide18
18exceRpt v3.1.9 in Genboree Workbench
Group
Database
Files
Tool Settings
Provide 3’ adapter sequence, if known
Set options for random barcodes – length and location
Upload custom
oligo
sequences or use previously uploaded
oligo
sequences
Select endogenous libraries for mapping
Change order of endogenous libraries
Set mapping options – mismatches, bowtie seed lengthChoose exogenous library alignmentsSlide19
19exceRpt v3.1.9 in Genboree WorkbenchSlide20
20Metadata for exRNA-seqSlide21
21exRNA MetadataSlide22
22exRNA Metadata in GenboreeKB UIMetadata Data Model in UINested tabbed spreadsheet formatSlide23
23Metadata Entry in GenboreeKB UI
Metadata Template
Questionnaire
Edit these fields
Answer these questionsSlide24
24Pathway analysis in Genboree WorkbenchSlide25
25Pathway analysis in Genboree WorkbenchSlide26
26Useful LinksexRNA Portalhttp://exrna.orgexRNA Portal Software
Resourceshttp://exrna.org/resources/software
exRNA
Atlas
http://genboree.org/exRNA-atlas/index.rhtml
Data Coordination
Center
Wiki
http
://
genboree.org/theCommons/projects/exrna-mads/wiki
exRNA Data Analysis
Tools
Wikihttp://genboree.org/theCommons/projects/exrna-tools-may2014/wikiSlide27
Acknowledgements27Baylor College of Medicine, Houston, TXAleksandar Milosavljevic, DirectorMatthew Roth, Co-DirectorElke Norwig-EastaughGenboree Dev Team at BaylorAndrew JacksonSameer PaithankarSai Lakshmi SubramanianNeethu ShahWilliam Thistlethwaite
Aaron Baker
Sponsored by:
Grant
1U54DA036134
from
the NIH Common Fund, through the Office of Strategic Coordination/Office of the NIH
Director
Yale University, New Haven, CT
Mark Gerstein
Joel
Rozowsky
Rob KitchenFabio NavarroGladstone Institutes, San Francisco, CAAlexander PicoAnders RiuttaKristina HanspersPacific Northwest Diabetes Research Institute, Seattle, WADavid GalasRoger Alexander