Fish546

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  • Mean 611 bp
  • Putting them on a wiki - ..8 cutters, and a 6 cutterApplications: SNPs per base pair for different functional groupsOther combinations of data: CpG ratios
  • Putting them on a wiki - ..8 cutters, and a 6 cutterApplications: SNPs per base pair for different functional groupsOther combinations of data: CpG ratios
  • Fish546

    1. 1. Facilitating analysis ofgenomic variation inOlympia oystersBioinformatics, FISH546Mackenzie Gavery3/14/13
    2. 2. GOALS• Utilize existing genomic resources (transcriptome) for RAD-Seq design• Generate useful generic feature files (gff) to facilitate functional annotation of SNPs• Generate a workflow for annotating synonymous and non-synonymous SNPs in a non-model species*
    3. 3. Methods• Starting material: • Transcriptome: 41,000 contigs • SNP Table (CLCBio) ~52,000 • Annotations: blastx, GO• Tools: • Galaxy • Excel • Blastx
    4. 4. Results Cut sites SNP w/in SNP w/in 50bp 100bp NotI 118 43 64 SbfI 600 177 177 EcoRI 19,996 3,905 12,733
    5. 5. Results Cut sites SNP w/in SNP w/in 50bp 100bp NotI 118 43 64 SbfI 600 177 177 EcoRI 19,996 3,905 12,733• New data tracks: • Gene ID • GO annotation sub-groups • SNPs • Blastx regions (with frame)
    6. 6. Applications• Assist with RAD-Seq experimental design• Ask interesting biological questions – are there differences in the number of SNPs in housekeeping v. inducible genes?
    7. 7. Next steps• Do these SNPs result in functional changes (i.e. do they change the protein)?1. Blastx custom output -outfmt “6 sseqid, qseqid, frames…”2. aachanges (Galaxy)
    8. 8. Next steps• Do these SNPs result in functional changes (i.e. do they change the protein)?1. Blastx custom output -outfmt “6 sseqid, qseqid, frames…”2. aachanges (Galaxy) SNP bed gene bed

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