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RGASP Gary Williams

RGASP Gary Williams. Exonerate vs cufflinks. Cufflinks vs MAQ. Exonerate vs MAQ. Comparing submitted models. Have submissions from groups: Gun, Mar, Tyl, Vic Want to look at models that are different. Fast way to find these is to look at RPKM expression levels. Typical expression levels.

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RGASP Gary Williams

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  1. RGASP Gary Williams

  2. Exonerate vs cufflinks

  3. Cufflinks vs MAQ

  4. Exonerate vs MAQ

  5. Comparing submitted models • Have submissions from groups: Gun, Mar, Tyl, Vic • Want to look at models that are different. • Fast way to find these is to look at RPKM expression levels.

  6. Typical expression levels RPKM of locus

  7. Want loci which differ • Took maximum RPKM of loci from each group. • Compare the RPKM levels to find genes where there is a big difference in one or more submissions. • Gun & Vic submissions have no mitochondrial genes, assume these were not looked at. • 4% of 20,000 loci no difference, 9% less than 50% difference, 76% have >50% difference, 13% have 100% difference (zero & not zero values).

  8. B0513.3 • Gun: 14,468 Mar: 4,337 Tyl: 1,145 Vic: 4,636 • Well formed, highly expressed, no problem

  9. B0412.4 • Gun: 9,629 Mar: 3,980 Tyl: 31 Vic: 3,738 • Well formed, highly expressed, snoRNAs in introns

  10. M01H9.1 • Gun: 33 Mar: 1 Tyl: 4 Vic: 24 • Well formed, medium expression, new isoform extending exon 3?

  11. F26F2.2 • Gun: 0.5 Mar: 0.1 Tyl: 0.03 Vic: 0.95 • Well formed, low expression, exons 1&2 not unique in genome, isoform starting at exon 3

  12. C05G5.7 • Gun: 155 Mar: 0 Tyl: 0 Vic: 121 • Well formed single exon, high expression.

  13. Y105C5A.12 • Gun: 182 Mar: 0 Tyl: 58 Vic: 223 • Copy of part of nearby gene, high expression.

  14. END

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