Spliced Transcripts Alignment to a Reference
(STAR) (cont.)
description, 117
fast alignment algorithm, 155
mapping command, 117
mapping job, 117
mapping multiple samples, 117
output, 156
read alignment/mapping, 156
reference index, 155
Splice-unaware aligners, 116
Splicing events, 5
SRA-toolkit, 92
Standard Phred quality score, 125, 139
Staphylococcus aureus, 53
STAR alignment tools, 106, 107
Strand bias filter, 132
Structural variants, 130, 131, 136
Systems medicine, 2
T
Tag directory, 183
Targeted sequencing, 11, 57
TCGA Network, 25, 30, 31
Therapeutic targets, 32
TopHat2, 150
gapped alignment, 154
genomic annotations, 152, 153
output, 155
read alignment/mapping, 153
reference Index, 153
spliced alignment, 154
transcriptome alignment, 153
unspliced alignment, 154
Traditional DNA sequencing technologies, 48
Transcription, 12
Transcription factor (TF), 179
Transcription factor binding sites (TFBS),
178, 189
Transcription start side (TSS), 187
Transcriptome alignment, 153
Transcriptomic characterization, 29
Transfer RNAs (tRNA), 146
Translation, 6
Transmission electron microscopy (TEM), 53
Trastuzumab, 29
Travis Glenn’s Field Guide to Next Generation
DNA Sequencer, 48
Trinity, 157, 158
Tumor-infiltrating lymphocytes (TILs), 29
Tumor mutational burden (TMB), 29
Tumor panels, 11
Tumor suppressor genes, 20, 33
U
UK Biobank, 32
Unit edit distance (edist), 113, 114
Untranslated regions (UTRs), 9
UV radiation, 22
V
Variant annotation, 135
Variant calling algorithms
Bayesian, 126–128
heuristic, 128, 130
naive, 125, 126
outputs VCF files, 132
Variant distance bias tests, 133
Variants of uncertain significance (VUS), 21
VCF (Variant Call Format), 91
Velvet, 157, 158
Visualization tools, 136
W
Whole genome sequencing (WGS), 10, 33
Whole-exome sequencing, 10, 26
Z
Zero-mode waveguides (ZMWs), 51
ZMW nanostructure arrays, 52
218
Index