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Slides from lecture that go over assembly and annotation of NGS data using local resources
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Transcriptomics
16 million~40 bp
HQ reads
16 million~40 bp
HQ reads
13Tuesday, January 26, 2010
raw data
14Tuesday, January 26, 2010
csfasta
15Tuesday, January 26, 2010
csfasta
16Tuesday, January 26, 2010
csfasta
17Tuesday, January 26, 2010
qual
18Tuesday, January 26, 2010
stats
19Tuesday, January 26, 2010
dealing with raw data
21Tuesday, January 26, 2010
dealing with raw data
22Tuesday, January 26, 2010
dealing with raw data
23Tuesday, January 26, 2010
dealing with raw data
24Tuesday, January 26, 2010
dealing with raw data
25Tuesday, January 26, 2010
dealing with raw data $$$$$$
26Tuesday, January 26, 2010
dealing with raw data $$$$$$
27Tuesday, January 26, 2010
dealing with raw data
28Tuesday, January 26, 2010
trimmed
Processed a total of 43490590 sequences. 27309944
sequences have been completely removed during
trimming. 1190442453
nucleotides have been trimmed,
altogether.
29Tuesday, January 26, 2010
ESTs Short Reads (ngs)
options:assemble (non-redundant)Blast SeparatelyAssemble on Reference (MAP/Variant)Assemble on Reference (RNAseq)
32Tuesday, January 26, 2010
ESTs
Assembly
33Tuesday, January 26, 2010
ngs
Assembly
34Tuesday, January 26, 2010
ngs - assembly open source
de novo
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ngs - assembly $$$
36Tuesday, January 26, 2010
ngs - assembly
37Tuesday, January 26, 2010
ngs - assembly
38Tuesday, January 26, 2010
ngs - assembly
39Tuesday, January 26, 2010
ngs - assembly
40Tuesday, January 26, 2010
ngs - assembly
41Tuesday, January 26, 2010
ngs - assembly
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ngs - assembly
9:39
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ngs - assembly
10:00
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assemble
45Tuesday, January 26, 2010
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assemble ngs cell
51Tuesday, January 26, 2010
assemble ngs cell
52Tuesday, January 26, 2010
assemble ngs cell
53Tuesday, January 26, 2010
output = consensus
ESTs ngs
56Tuesday, January 26, 2010
ESTs Short Reads (ngs)
options:assemble (non-redundant)Blast SeparatelyAssemble on Reference (MAP/Variant)Assemble on Reference (RNAseq)
57Tuesday, January 26, 2010
annotation
59Tuesday, January 26, 2010
annotation
60Tuesday, January 26, 2010
annotation
61Tuesday, January 26, 2010
annotation
62Tuesday, January 26, 2010
default
64Tuesday, January 26, 2010
changes
66Tuesday, January 26, 2010
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data management
relational databases
very large files
73Tuesday, January 26, 2010
data management
74Tuesday, January 26, 2010
data management
75Tuesday, January 26, 2010
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