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SNP Workshop III
NGS and SNP Discovery
NGS and SNP Discovery
!
Challenges
Sharing
NGS and SNP Discovery
NGS and SNP Discovery
NGS and SNP Discovery
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NGS and SNP Discovery
credit: NOAA
SNP Discovery in Pacific herring using 454 transcriptome sequencing
Steven Roberts, Jim Seeb, Lisa Seeb, Lorenz Hauser,University of WashingtonSchool of Aquatic and Fishery SciencesWilliam TemplinAlaska Division of Fish and GameDivision of Commercial Fisheries
Exxon Valdez Oil Spill Trustee Council
Credit: EXXON VALDEZ Oil Spill Trustee Council
Togiak
Kodiak
Prince William Sound
Sitka
Approach
• Pooled Individuals to generate 2 libraries
• Liver• Testes
• De novo Assembly
• Annotation
• SNP Discovery
Sequencing Output (combined)
Reads: 1.9 millionAverage Length: 272 bp
Matched: 1.7 millionContigs: 47,267Average Length of Contigs: 728 bp
Comparing Tissues
14190 featuresnot expressed
in Testes
10622 features not expressed
in Liver
Annotation (combined)
!
SNP Discovery
16,000 SNPs
per library - ~9300 SNPs
!
Annotation of corresponding
features!
=
all features
SNP Discovery
!
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SNP Discovery
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tinyurl.com/herringSNP
Targeting SNPs
!
xenobiotic response
Synonymous and NonSynonymous
consensussequences
workflow
EMBOSSgetorf
referenceassembly
SNPDetection
AnnotateSNP Positive
Features
Filter based
on e-value 7017 SNPs
2514 NonSynonymous
Synonymous and NonSynonymous workflow
2514 NonSynonymous
NonSynonymous
NonSynonymous
stress response
