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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
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raw data
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csfasta
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csfasta
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csfasta
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qual
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stats
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dealing with raw data
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dealing with raw data
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dealing with raw data
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dealing with raw data
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dealing with raw data
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dealing with raw data $$$$$$
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dealing with raw data $$$$$$
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dealing with raw data
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trimmed
Processed a total of 43490590 sequences. 27309944
sequences have been completely removed during
trimming. 1190442453
nucleotides have been trimmed,
altogether.
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ESTs Short Reads (ngs)
options:assemble (non-redundant)Blast SeparatelyAssemble on Reference (MAP/Variant)Assemble on Reference (RNAseq)
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ESTs
Assembly
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ngs
Assembly
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ngs - assembly open source
de novo
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ngs - assembly $$$
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ngs - assembly
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ngs - assembly
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ngs - assembly
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ngs - assembly
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ngs - assembly
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ngs - assembly
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ngs - assembly
9:39
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ngs - assembly
10:00
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assemble
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assemble ngs cell
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assemble ngs cell
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assemble ngs cell
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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)
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annotation
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annotation
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annotation
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annotation
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default
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changes
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data management
relational databases
very large files
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data management
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data management
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