Download Williams_worm_evaluation

RGASP
Gary Williams
Exonerate vs cufflinks
exonerate vs cufflinks
exonerate vs cufflinks
5
6
4
5
4
3
3
1
0
-4
-3
-2
-1
0
1
-1
2
3
4
Log10 cufflinks
Log10 cufflinks
2
2
1
0
-4
-3
-2
-1
0
1
-1
-2
-2
-3
-3
-4
Log10 exonerate
-4
Log10 exonerate
2
3
4
Cufflinks vs MAQ
cufflinks vs MAQ
4
4
3
3
2
2
1
1
0
-4
-2
0
2
4
6
MAQ
Log10 MAQ
cufflinks vs MAQ
0
-4
-2
0
-1
-1
-2
-2
-3
-3
-4
-4
Log10 cufflinks
2
cufflinks
4
6
Exonerate vs MAQ
exonerate vs MAQ
4
4
3
3
2
2
1
1
0
-4
-3
-2
-1
0
1
2
3
4
MAQ
Log10 MAQ
exonerate vs MAQ
0
-4
-3
-2
-1
0
-1
-1
-2
-2
-3
-3
-4
-4
Log10 exonerate
exonerate
1
2
3
4
Comparing submitted models
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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
RPKM frequency
5000
4500
4000
3500
3000
2500
2000
1500
1000
500
0
0
200
400
600
800
RPKM of locus
1000
1200
1400
Want loci which differ
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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).
B0513.3

Gun: 14,468 Mar: 4,337 Tyl: 1,145 Vic: 4,636
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Well formed, highly expressed, no problem
B0412.4
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Gun: 9,629 Mar: 3,980 Tyl: 31 Vic: 3,738
Well formed, highly expressed, snoRNAs in
introns
M01H9.1


Gun: 33 Mar: 1 Tyl: 4 Vic: 24
Well formed, medium expression, new isoform
extending exon 3?
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
C05G5.7

Gun: 155 Mar: 0 Tyl: 0 Vic: 121

Well formed single exon, high expression.
Y105C5A.12

Gun: 182 Mar: 0 Tyl: 58 Vic: 223

Copy of part of nearby gene, high expression.
END