- 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 10 and 11: Sequencing by ligation (ABI Sol
- Page 12 and 13: Metzker, Nat Rev Gene1cs, 11(1)
- Page 16 and 17: Single-‐molecule real-‐tim
- Page 18 and 19: Cluster amplificaIon 1st cut FL
- Page 20 and 21: Barcoding ì © Illumina
- Page 22 and 23: Different chemistries yield diff
- Page 24 and 25: (Pre-‐)Phasing a source of
- Page 26 and 27: CLC Bio, Annual Survey (2012)
- Page 28 and 29: NGS mostly applied toward basic
- Page 30 and 31: FASTQ format @SEQ_ID GATTTGGGGTTC
- Page 32 and 33: Phred quality scores are linked
- Page 34 and 35: Wikipedia Quality scores vary b
- Page 36 and 37: Hash table Hash FuncIon Key 1
- Page 38 and 39: Spaced-‐seed • Cut each po
- Page 40 and 41: Ambiguous reads read reference
- Page 42 and 43: 0-‐based vs. 1-‐based co
- Page 44 and 45: Direct comparison of aligners d
- Page 46 and 47: Simulated 2 mil . C. elegans
- Page 48 and 49: cross_match & NovoAlign PE plac
- Page 50 and 51: Repeated with real data from t
- Page 52 and 53: Top Performing Aligners Alignmen
- Page 54 and 55: Bioo Scien1fic Corp. Whole geno
- Page 56 and 57: Read depth as a function of f
- Page 58 and 59: Genotype Calling -‐ GATK
- Page 60 and 61: GATK vs. Illumina
- Page 62 and 63: ChIP sequencing
- Page 64 and 65:
Two fundamental types of peaks
- Page 66 and 67:
Different number of peaks ident
- Page 68 and 69:
Lister et al., Genome Research,
- Page 70 and 71:
Conversion yields up to four p
- Page 72 and 73:
Akalin et al., Genome Biology,
- Page 74 and 75:
Definitions ì RNA = class of
- Page 76 and 77:
RNA molecules 1. fragmentation of R
- Page 78 and 79:
Composition of RNA depends upon
- Page 80 and 81:
Silica membrane enriches for RN
- Page 82 and 83:
Zeugin JA & Hartley JL, Focus
- Page 84 and 85:
Genebody coverage across degrade
- Page 86 and 87:
Gene-‐expression comparison o
- Page 88 and 89:
Capturing stem-‐loop mRNA 20
- Page 90 and 91:
Bogdanova et al., Molecular Bio
- Page 92 and 93:
Abundant transcript measurements
- Page 94 and 95:
Fragmentation of oligo-‐dT p
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Positional bias caused by choic
- Page 98 and 99:
Quality assesment ì Levin et
- Page 100 and 101:
Did you QC the data? no yes QC the
- Page 102 and 103:
Dobin et al., Bioinforma1cs, 29
- Page 104 and 105:
STAR vs Tophat ì ì ì STAR ma
- Page 106 and 107:
Mar1n et al., Nature Reviews G
- Page 108 and 109:
Methods of quantifying gene exp
- Page 110 and 111:
Accurate quantification requires
- Page 112 and 113:
More sophisticated normalization
- Page 114 and 115:
Different normalization methods
- Page 116 and 117:
DEGs in common for each of th
- Page 118 and 119:
GAPDH isn’t much of a ‘hou
- Page 120 and 121:
'The property of being one and
- Page 122 and 123:
Script limitations 1) Linear exe
- Page 124 and 125:
Maintain a bioinformatics journa
- Page 126 and 127:
Empirical dialectical method p