Investigation of Genomic Variation in the Rising Era of Individual Genome Sequence: A Primer on Some Available Datasets and Structures
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1 Investigation of Genomic Variation in the Rising Era of Individual Genome Sequence: A Primer on Some Available Datasets and Structures September 28, 2015
2 A 10,000 Foot View Genomics Data at NCBI Organizational Thoughts: Genomics terminology Health Resources Bioproject and SRA BLASTing into SRA What is dbgap? Reference Genomes Obtaining Large Datasets More Information and Data Science Challenges!
3 Review of terminology and concepts How Genomes are Assembled and Mapped Martine Zilversmit 2013
4 Review of terminology and concepts How Genomes are Assembled and Mapped
5 Tuberculosis
6 ClinVar
7 ClinVar
8 ClinVar
9 ClinVar
10 ClinVar
11 Variation Viewer
12 Variation Viewer
13 Gene
14 Gene
15 Tuberculosis
16 GTR
17 Tuberculosis
18 BioProject
19 BioProject
20 BioProject New Data Every Day!
21 BioProject
22 SRA
23 SRA
24 SRA
25
26
27 SRA
28 Bioproject
29 SRA
30 SRA
31 SRA
32 Why SRA? sam-dump aligned-region 17: SRR > BRCA1.sam
33 Why SRA?
34 The SRA Toolkit!
35 now with an SDK!
36 Toolkit SDK and Toolkit Spark!
37 and its available in Galaxy!
38 Blasting into SRA
39 Blasting into SRA
40 Blasting into SRA
41 Blasting into SRA
42 Blasting into SRA
43 Blasting into SRA
44 Blasting into SRA
45 Blasting into SRA
46 Blasting into SRA
47 Blasting into SRA
48 Blasting into SRA
49 Blasting into SRA
50 Blasting into SRA
51 Blasting into SRA
52 Blasting into SRA
53 LATF (SRA) Loader for vdb-blast!
54 Generally Cool Stuff
55 MOLE-BLAST: BLAST for Metagenomics
56 What is dbgap?
57 What is dbgap? Genome Variation Phenotype Medicine PubMed and PubMed Central Genome Browser SRA dbmhc PheGenI Gene GEO GenBank dbsnp dbgap GTR RefSeq ClinVar MedGen Trace Archive dbvar OMIM
58 What is dbgap? Samples 1,238,033 1,102, , , , ,193 70, , ,
59 What is dbgap? Subjects 1,002, , , , , , ,311 14,201 53,
60 What is dbgap? GERA cohort
61 What is dbgap?
62 What is dbgap?
63 What is dbgap?
64 Data Context Query refinement filters
65 Data Preview
66 Data Preview Individual details are available with approved access to the study Samples discovered by the beacon can then be passed to viewers, downloaded, processed with the SRA toolkit, etc. for further analysis.
67 What is dbgap?
68 What is dbgap?
69 Background sets
70 Reference Genomes
71 Human Reference Genome
72 Reference Genomes -- Mycobacteria
73 Where to Get the Genomes
74 Where to Get the Genomes
75 Where to Get the Genomes
76 Reference Genomes (Mycobacteria)
77 Reference Genomes (Mycobacteria) For every Refseq and Genbank genome.fasta file, we have changed the headers such that they are compatible with popular RNAseq software
78 Status of Prokaryotic Genomes Assemblies On 7/13/2015: 38,077 prokaryotic RefSeq assemblies: <ncbi>/assembly/?term=prokaryotes[organism] Level of completion: Complete: 4276 The rest as scaffold or contigs NCBI Reference Sequence staff generates RefSeq genome records for most of the submitted prokaryotic assemblies In May 2015, the NCBI RefSeq group completed a major step towards transition to a new model of processing and annotating prokaryotic genomes. 78
79 Non-redundant WP_ Proteins NP_ =WP_ NP_ =WP_ YP_ = WP_ YP_ = WP_ YP_ = WP_ Annotated on reference genomes: NP_ = identical to WP_ YP_ = identical to WP_ YP_ = identical to WP_
80 The New Model Introduces Different Categories of RefSeq Genomes RefSeq reference Genomes genomes of high quality sequence and annotation Currently 122 genomes PGAP annotation + curation by NCBI staff and collaborators NP_ ; YP_ , and YP_ are all annotated on the reference genomes; they are cross-referenced to WP_ , and have corresponding Gene records RefSeq representative Genomes High quality: mostly complete, but some at scaffold assembly level Annotated with WP_ proteins Some link to Gene RefSeq variant Genomes Scaffold or contigs assembly level Annotated with WP_ proteins Do not link to Gene 80
81 How the Genomes are Annotated
82 De novo RNAseq Assembly
83 RNAseq in the Wild
84 Normalizing Large Dataset Comparison Check data quality Current largest source of noise is library prep Setting parameters (or not) Remember multiple etiologies If it looks like a duck Multiple testing correction Not Bonferroni Validation can come in many forms (as long as its independent)
85 Variant Calling Filtering GWAS Eutils Access to Large Datasets Thoughts on Efficient Computation for Large Datasets Keep (updated) databases in a central respository Write scripts such that databases (for example BLASTdbs) are kept in memory Keep versioned toolsets in a central repository
86 ClinVar FTP
87 dbsnp FTP
88 PhegenI
89 Last Topic -- Eutils Full slide set and supplementary materials, including scripts, available at: ftp://ftp.ncbi.nlm.nih.gov/pub/education/public_webinars/2014/oct_eutils/ Video available soon at:
90 Entrez Databases and UIDs 10/15/14 90
91 The E-utilities eutil.fcgi? esearch.fcgi? egquery.fcgi? esummary.fcgi? einfo.fcgi? efetch.fcgi? elink.fcgi? epost.fcgi?
92 What do the E-utilities do? text query ESearch set of UIDs set of UIDs ESummary Record summaries set of UIDs EFetch Full data records set of UIDs in db A ELink set of UIDs in db B set of UIDs EPost temporary storage Entrez history 92
93 Or An Easier Way Introducing Entrez Direct The E-utilities on the UNIX command line esearch db gene query foxp2[gene] AND human[orgn] \ elink target protein name gene_protein_refseq \ efetch format fasta ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/ 93
94 The dbgap Data Browser (DDB)
95 More Detailed Information About NCBI Resources! Subscribe to our YouTube Channel!
96 Example Data Science Challenges! Extract reference genome from.sam header out of SRA toolkit and download this automatically! There are 42,644 Public Runs as of 9/27/2015 (105 K Controlled Access) e.g. $TOOLKIT/sam-dump SRR head -25 (The problem is that for ambiguous accessions, you have to make a clever guess based on sequence length) AND/OR If there is no reference genome for a given set of samples, realign them to genomes automatically and resubmit them. Here s an example! Contact:
This software/database/presentation is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part
This software/database/presentation is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government
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The i5k a pan-arthropoda Genome Database. Chris Childers and Monica Poelchau USDA-ARS, National Agricultural Library
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Chimp Sequence Annotation: Region 2_3
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BLASTing through the kingdom of life
Information for students Instructions: In short, you will copy one of the sequences from the data set, use blastn to identify it, and use the information from your search to answer the questions below.