next-generation sequencing & analysis - Chagall

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Metzker, Nat Rev Gene1cs, 11(1):31-‐46 (2010) Template Immobilization Strategies
Page 1 and 2: Next-‐gen. sequencing and an
Page 3 and 4: Two major (interconnected) theme
Page 5 and 6: Chain termination DeoxynucleoIdes
Page 7: Sanger sequencing - simple exam
Page 11 and 12: Di-‐base encoding AT
Page 13 and 14: Metzker, Nat Rev Gene1cs, 11(1)
Page 15 and 16: Metzker, Nat Rev Gene1cs, 11(1)
Page 17 and 18: Glenn, Molecular Ecology, 11(5):
Page 19 and 20: Paired-‐end sequencing is go
Page 21 and 22: Auer et al., Gene1cs, 185(2):40
Page 23 and 24: Substitution errors are platform
Page 25 and 26: Glenn, Molecular Ecology, 11(5):
Page 27 and 28: CLC Bio, Annual Survey (2012)
Page 29 and 30: Aligners and alignment ì Image
Page 31 and 32: Illumina sequence identifiers (C
Page 33 and 34: Quality scores useful for… ì
Page 35 and 36: Two main types of alignment ag
Page 37 and 38: Bananas ananas nanas anas nas
Page 39 and 40: Burrows-‐Wheeler transform
Page 41 and 42: Sequence Alignment/Map (SAM) for
Page 43 and 44: 70 short-‐read aligners u u
Page 45 and 46: Koboldt, MassGenomics 10 aligner
Page 47 and 48: Koboldt, MassGenomics CPU time
Page 49 and 50: SNPs greater influence than inf
Page 51 and 52: Read Placement Results for ~2
Page 53 and 54: Mark Watson, Roslin Ins1tute Th
Page 55 and 56: Fragmentation method biases cove
Page 57 and 58: Commonly Used Framework for Cal
Page 59 and 60:
Genotype calling -‐ Illumina
Page 61 and 62:
SNP calling - best practices 1
Page 63 and 64:
Motif finding in tag enriched
Page 65 and 66:
ChIP-‐seq peak calling progr
Page 67 and 68:
Wilbanks et al., PLoS One, 5(7
Page 69 and 70:
Bisulfite conversion ì
Page 71 and 72:
Krueger & Andrews, Bioinforma1cs
Page 73 and 74:
Transcriptome sequencing ì a.k.
Page 75 and 76:
Technique workflow RNA isolaIon
Page 77 and 78:
Major classes of RNA Type (%
Page 79 and 80:
Different extraction techniques
Page 81 and 82:
“RNA was extracted from the
Page 83 and 84:
Schroeder et al., BMC Mol Biol
Page 85 and 86:
Removal of ribosomal RNA Indire
Page 87 and 88:
Abundance of non-‐coding tra
Page 89 and 90:
Poly(A)+ vs. ribo-‐: genebod
Page 91 and 92:
Yi et al., Nucleic Acid Resear
Page 93 and 94:
Divalent cations promote RNA de
Page 95 and 96:
Not-‐so-‐random ‘random
Page 97 and 98:
Levin et al., Nature Methods 7
Page 99 and 100:
dUTP most correlated with array
Page 101 and 102:
Trapnell et al., Bioinforma1cs,
Page 103 and 104:
STAR vs. TopHat
Page 105 and 106:
Mar1n et al., Nature Reviews G
Page 107 and 108:
TopHat manual Read the docs!
Page 109 and 110:
Credit: Simon Anders (HTSeq) Ov
Page 111 and 112:
Reads per kilobase of exon mod
Page 113 and 114:
Normalization procedure has a p
Page 115 and 116:
Dillies et al., Brief Bioinform
Page 117 and 118:
Summary of the normalization me
Page 119 and 120:
Soneson & Delorenzi, BMC Bioinf
Page 121 and 122:
Broadly useful Linux tools / s
Page 123 and 124:
Structure of a makefile ! Gener
Page 125 and 126:
More basic research to be done
Page 127:
Closing ì Knowledge is not a
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