Comparative Gene-Expression Analysis III Sequence-based techniques (0420)

Index

00:00 1.
Other Sequencing Technology
02:24 2.
BioNano Genomics (Irys System)
05:56 3.
Overview of RNA-seq Library Construction
08:29 4.
RNA Sample Preparation
12:04 5.
RNA Quality Assessment: Agilent 2100 BioAnalyzer (RIN)RNA Quantification:The UV-absorbance method uses a spectrophotometer to measure the natural absorbance of light at 260 nm (for DNA and RNA) or 280 nm (for proteins)(A260 - A320) x RNA extinction coeffi
14:23 6.
Input : 10 pg – 10 ng total RNA (RIN>8)
15:52 7.
QC / Demultiplexing
18:01 8.
Coverage
21:17 9.
NGS Experimental Considerations
24:54 10.
Phred - Quality Base Calling
26:33 11.
Phred Qualities
28:40 12.
N50 / L50
33:01 13.
Quality Control
36:06 14.
Quality Control – FastQC Tool for Quality Visualization
38:38 15.
Quality Control – FastQC Tool for Quality Visualization
40:08 16.
Quality Control – FastQC Tool for Quality Visualization
40:29 17.
Quality Control – FastQC Tool for Quality Visualization
40:55 18.
Quality Control – FastQC Tool for Quality Visualization
41:32 19.
PCR Duplicate
42:35 20.
Adapter Removal
43:30 21.
Example
44:32 22.
QC / Demultiplexing
46:05 23.
Differences Between RNA-Seq and DNA-Seq
47:19 24.
Alignment
48:14 25.
The Seed-Filter-Extend Approach
48:33 26.
Hash-Based Alignment Methods
50:59 27.
Burrows–Wheeler Transform
56:22 28.
Assembly
58:38 29.
Problems in DNA Sequencing
1:00:45 30.
Assemble algorithms
1:01:29 31.
de Bruijn Graph Approach
1:03:27 32.
de Bruijn Graph Approach
1:04:03 33.
QC / Demultiplexing
1:05:09 34.
RNA-Seq Data Normalization Methods
1:07:42 35.
RPKM
1:07:57 36.
Question
1:08:12 37.
Drawbacks of R/FPKM
1:14:38 38.
Evaluation of Normalization Methods
1:15:57 39.
Workflow for Analysis of RNA-Seq Data
1:16:27 40.
Tuxedo Pipeline
1:17:51 41.
Strategies for Reconstructing Transcripts from RNA-Seq Reads
1:18:29 42.
Differential Analysis
1:19:26 43.
Improving the Human Reference Genome
1:21:28 44.
Single Cell Database
1:23:12 45.
Single Sample GSEA (ssGSEA)
1:24:53 46.
GSVA Algorithm
1:28:31 47.
GSVA Algorithm
1:34:05 48.
Tools for NGS Data Analysis
1:34:09 49.
ONLINE ANALYSIS TOOLShttp://molbiol-tools.ca/
1:34:13 50.
Online Bioinformatics Resources Collection (OBRC)
1:34:27 51.
Tools for Visualizing Short Read Data
1:34:42 52.
Summary
1:35:06 53.
Microarrays vs RNA-seq
1:36:24 54.
Application of Sequence Census Assays

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Comment

00:00 1.
Other Sequencing Technology
02:24 2.
BioNano Genomics (Irys System)
05:56 3.
Overview of RNA-seq Library Construction
08:29 4.
RNA Sample Preparation
12:04 5.
RNA Quality Assessment: Agilent 2100 BioAnalyzer (RIN)RNA Quantification:The UV-absorbance method uses a spectrophotometer to measure the natural absorbance of light at 260 nm (for DNA and RNA) or 280 nm (for proteins)(A260 - A320) x RNA extinction coeffi
14:23 6.
Input : 10 pg – 10 ng total RNA (RIN>8)
15:52 7.
QC / Demultiplexing
18:01 8.
Coverage
21:17 9.
NGS Experimental Considerations
24:54 10.
Phred - Quality Base Calling
26:33 11.
Phred Qualities
28:40 12.
N50 / L50
33:01 13.
Quality Control
36:06 14.
Quality Control – FastQC Tool for Quality Visualization
38:38 15.
Quality Control – FastQC Tool for Quality Visualization
40:08 16.
Quality Control – FastQC Tool for Quality Visualization
40:29 17.
Quality Control – FastQC Tool for Quality Visualization
40:55 18.
Quality Control – FastQC Tool for Quality Visualization
41:32 19.
PCR Duplicate
42:35 20.
Adapter Removal
43:30 21.
Example
44:32 22.
QC / Demultiplexing
46:05 23.
Differences Between RNA-Seq and DNA-Seq
47:19 24.
Alignment
48:14 25.
The Seed-Filter-Extend Approach
48:33 26.
Hash-Based Alignment Methods
50:59 27.
Burrows–Wheeler Transform
56:22 28.
Assembly
58:38 29.
Problems in DNA Sequencing
1:00:45 30.
Assemble algorithms
1:01:29 31.
de Bruijn Graph Approach
1:03:27 32.
de Bruijn Graph Approach
1:04:03 33.
QC / Demultiplexing
1:05:09 34.
RNA-Seq Data Normalization Methods
1:07:42 35.
RPKM
1:07:57 36.
Question
1:08:12 37.
Drawbacks of R/FPKM
1:14:38 38.
Evaluation of Normalization Methods
1:15:57 39.
Workflow for Analysis of RNA-Seq Data
1:16:27 40.
Tuxedo Pipeline
1:17:51 41.
Strategies for Reconstructing Transcripts from RNA-Seq Reads
1:18:29 42.
Differential Analysis
1:19:26 43.
Improving the Human Reference Genome
1:21:28 44.
Single Cell Database
1:23:12 45.
Single Sample GSEA (ssGSEA)
1:24:53 46.
GSVA Algorithm
1:28:31 47.
GSVA Algorithm
1:34:05 48.
Tools for NGS Data Analysis
1:34:09 49.
ONLINE ANALYSIS TOOLShttp://molbiol-tools.ca/
1:34:13 50.
Online Bioinformatics Resources Collection (OBRC)
1:34:27 51.
Tools for Visualizing Short Read Data
1:34:42 52.
Summary
1:35:06 53.
Microarrays vs RNA-seq
1:36:24 54.
Application of Sequence Census Assays

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Comparative Gene-Expression Analysis III Sequence-based techniques (0420)

Duration: 1:37:12, Browse: 411, Last Updated: 2021-04-21

Prev Next

00:00 1.
Other Sequencing Technology
02:24 2.
BioNano Genomics (Irys System)
05:56 3.
Overview of RNA-seq Library Construction
08:29 4.
RNA Sample Preparation
12:04 5.
RNA Quality Assessment: Agilent 2100 BioAnalyzer (RIN)RNA Quantification:The UV-absorbance method uses a spectrophotometer to measure the natural absorbance of light at 260 nm (for DNA and RNA) or 280 nm (for proteins)(A260 - A320) x RNA extinction coeffi
14:23 6.
Input : 10 pg – 10 ng total RNA (RIN>8)
15:52 7.
QC / Demultiplexing
18:01 8.
Coverage
21:17 9.
NGS Experimental Considerations
24:54 10.
Phred - Quality Base Calling
26:33 11.
Phred Qualities
28:40 12.
N50 / L50
33:01 13.
Quality Control
36:06 14.
Quality Control – FastQC Tool for Quality Visualization
38:38 15.
Quality Control – FastQC Tool for Quality Visualization
40:08 16.
Quality Control – FastQC Tool for Quality Visualization
40:29 17.
Quality Control – FastQC Tool for Quality Visualization
40:55 18.
Quality Control – FastQC Tool for Quality Visualization
41:32 19.
PCR Duplicate
42:35 20.
Adapter Removal
43:30 21.
Example
44:32 22.
QC / Demultiplexing
46:05 23.
Differences Between RNA-Seq and DNA-Seq
47:19 24.
Alignment
48:14 25.
The Seed-Filter-Extend Approach
48:33 26.
Hash-Based Alignment Methods
50:59 27.
Burrows–Wheeler Transform
56:22 28.
Assembly
58:38 29.
Problems in DNA Sequencing
1:00:45 30.
Assemble algorithms
1:01:29 31.
de Bruijn Graph Approach
1:03:27 32.
de Bruijn Graph Approach
1:04:03 33.
QC / Demultiplexing
1:05:09 34.
RNA-Seq Data Normalization Methods
1:07:42 35.
RPKM
1:07:57 36.
Question
1:08:12 37.
Drawbacks of R/FPKM
1:14:38 38.
Evaluation of Normalization Methods
1:15:57 39.
Workflow for Analysis of RNA-Seq Data
1:16:27 40.
Tuxedo Pipeline
1:17:51 41.
Strategies for Reconstructing Transcripts from RNA-Seq Reads
1:18:29 42.
Differential Analysis
1:19:26 43.
Improving the Human Reference Genome
1:21:28 44.
Single Cell Database
1:23:12 45.
Single Sample GSEA (ssGSEA)
1:24:53 46.
GSVA Algorithm
1:28:31 47.
GSVA Algorithm
1:34:05 48.
Tools for NGS Data Analysis
1:34:09 49.
ONLINE ANALYSIS TOOLShttp://molbiol-tools.ca/
1:34:13 50.
Online Bioinformatics Resources Collection (OBRC)
1:34:27 51.
Tools for Visualizing Short Read Data
1:34:42 52.
Summary
1:35:06 53.
Microarrays vs RNA-seq
1:36:24 54.
Application of Sequence Census Assays

Location

Folder name

2021

Author

賴亮全

Branch

賴亮全教授

Created

2021-04-20 16:17:17

Last Updated

2021-04-21 10:47:48

Duration

1:37:12