RStudio, 66
terminal, 61
Conda, 63
Continuous long-read (CLR), 52, 53
Control-FREEC (7), 184
Copy number variation (CNV), 184
Counting reads per exons, 164
CpG islands, 9, 10
Cufflinks, 163
Cutadapt, 148
D
de Bruijn graphs, 157
De novo assembly
advantage, 157
contigs creation, 156
de Bruijn graphs, 157
gene expression analysis, 157
hybrid methods, 157
reference-based alignment, 157
RNA-Seq analysis, 157
tools, 157
Trinity, 157
contig generation, 159
de Bruijn graphs, 158, 159
output, 159
Velvet/Oases
Bruijn graph creation, 157
contig generation, 158
genome assembler, 157
output, 158
De novo genetic variants, 11, 12, 133, 134
Deconvolution methods, 28
Degenerate/redundant, 6
Deoxynucleoside triphosphate (dNTP), 49, 51, 52
Deoxyribonucleic acid (DNA)
alternating molecules, 3
biological information, 2
directionality, 3
gene transcription, 4
genetic code, 3, 5
labeled arbitrary, 3
protein production, 4
purpose, 4
RNA (see Ribonucleic acid (RNA))
sequence TGCCA, 3
transcription, 3
DESeq2, 166, 167
DEXSeq, 164
Differential expression (DE) analysis
BAM Files, 166
Cufflinks, 167
DESeq2, 167
individual count files, 166
linear models, 166
multivariate statistical methods, 166
pre-existing count table, 167
quantitative levels, transcripts/exons, 166
Disease-causing, 134, 136
DNA amplification, 56
DNA breaks, 22
DNA methylation, 179
DNA methylation (methyl-Seq), 10
DNA mismatch repair system, 29
DNA sequencing approaches, 43
DNA sequencing methods collection, 11
DNA/cDNA fragments, 42, 43
Driver mutations, 18
cancer driver genes, 19
gene fusions, 20
oncogenes, 19, 20
tumor suppressor, 20
E
Encyclopedia of DNA Elements (ENCODE), 6
End-distance bias filters, 133
Epigenetic modifications, 179
Epigenetic sequencing approaches, 178
Epigenetics, 9
Expectation maximization (EM) approach, 163
F
FASTA format
BLAST search, 81
scripting languages, 81
text-based format, 81
text-processing tools, 81
FASTA program suite, 113
FASTQ, 153
FASTQ format
ASCII table, 83
Phred Score, 83
Quality Check (see Quality Check via FastQC
program)
sequencing read, 82
text-based standard format, 82
FastQC, 148
Fetal chromosomal aneuploidies, 32
File formats
BAM file, 86, 87
BED format, 88, 89
BedGraph (*.bg) format, 90
FASTA format, 81
FASTQ, 82
fragment, 80
Index
213
terminal, 61
Conda, 63
Continuous long-read (CLR), 52, 53
Control-FREEC (7), 184
Copy number variation (CNV), 184
Counting reads per exons, 164
CpG islands, 9, 10
Cufflinks, 163
Cutadapt, 148
D
de Bruijn graphs, 157
De novo assembly
advantage, 157
contigs creation, 156
de Bruijn graphs, 157
gene expression analysis, 157
hybrid methods, 157
reference-based alignment, 157
RNA-Seq analysis, 157
tools, 157
Trinity, 157
contig generation, 159
de Bruijn graphs, 158, 159
output, 159
Velvet/Oases
Bruijn graph creation, 157
contig generation, 158
genome assembler, 157
output, 158
De novo genetic variants, 11, 12, 133, 134
Deconvolution methods, 28
Degenerate/redundant, 6
Deoxynucleoside triphosphate (dNTP), 49, 51, 52
Deoxyribonucleic acid (DNA)
alternating molecules, 3
biological information, 2
directionality, 3
gene transcription, 4
genetic code, 3, 5
labeled arbitrary, 3
protein production, 4
purpose, 4
RNA (see Ribonucleic acid (RNA))
sequence TGCCA, 3
transcription, 3
DESeq2, 166, 167
DEXSeq, 164
Differential expression (DE) analysis
BAM Files, 166
Cufflinks, 167
DESeq2, 167
individual count files, 166
linear models, 166
multivariate statistical methods, 166
pre-existing count table, 167
quantitative levels, transcripts/exons, 166
Disease-causing, 134, 136
DNA amplification, 56
DNA breaks, 22
DNA methylation, 179
DNA methylation (methyl-Seq), 10
DNA mismatch repair system, 29
DNA sequencing approaches, 43
DNA sequencing methods collection, 11
DNA/cDNA fragments, 42, 43
Driver mutations, 18
cancer driver genes, 19
gene fusions, 20
oncogenes, 19, 20
tumor suppressor, 20
E
Encyclopedia of DNA Elements (ENCODE), 6
End-distance bias filters, 133
Epigenetic modifications, 179
Epigenetic sequencing approaches, 178
Epigenetics, 9
Expectation maximization (EM) approach, 163
F
FASTA format
BLAST search, 81
scripting languages, 81
text-based format, 81
text-processing tools, 81
FASTA program suite, 113
FASTQ, 153
FASTQ format
ASCII table, 83
Phred Score, 83
Quality Check (see Quality Check via FastQC
program)
sequencing read, 82
text-based standard format, 82
FastQC, 148
Fetal chromosomal aneuploidies, 32
File formats
BAM file, 86, 87
BED format, 88, 89
BedGraph (*.bg) format, 90
FASTA format, 81
FASTQ, 82
fragment, 80
Index
213