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diff --git a/manuscript/1-Introduction.md b/manuscript/1-Introduction.md
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+# 1 Introduction
+
+{type: iframe, title:1 Introduction, width:800, height:600, poster:resources/chapt_screen_images/introduction.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/introduction.html)
+
+
+
diff --git a/manuscript/10-Whole-Genome-or-Exome-Sequencing.md b/manuscript/10-Whole-Genome-or-Exome-Sequencing.md
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+# 10 Whole Genome or Exome Sequencing
+
+{type: iframe, title:10 Whole Genome or Exome Sequencing, width:800, height:600, poster:resources/chapt_screen_images/whole-genome-or-exome-sequencing.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/whole-genome-or-exome-sequencing.html)
+
+
+
diff --git a/manuscript/11-RNA-Methods-Overview.md b/manuscript/11-RNA-Methods-Overview.md
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+# 11 RNA Methods Overview
+
+{type: iframe, title:11 RNA Methods Overview, width:800, height:600, poster:resources/chapt_screen_images/rna-methods-overview.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/rna-methods-overview.html)
+
+
+
diff --git a/manuscript/12-Bulk-RNA-seq.md b/manuscript/12-Bulk-RNA-seq.md
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+# 12 Bulk RNA-seq
+
+{type: iframe, title:12 Bulk RNA-seq, width:800, height:600, poster:resources/chapt_screen_images/bulk-rna-seq-1.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/bulk-rna-seq-1.html)
+
+
+
diff --git a/manuscript/13-Single-cell-RNA-seq.md b/manuscript/13-Single-cell-RNA-seq.md
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+# 13 Single-cell RNA-seq
+
+{type: iframe, title:13 Single-cell RNA-seq, width:800, height:600, poster:resources/chapt_screen_images/single-cell-rna-seq.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/single-cell-rna-seq.html)
+
+
+
diff --git a/manuscript/14-Spatial-transcriptomics.md b/manuscript/14-Spatial-transcriptomics.md
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+# 14 Spatial transcriptomics
+
+{type: iframe, title:14 Spatial transcriptomics, width:800, height:600, poster:resources/chapt_screen_images/spatial-transcriptomics-1.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/spatial-transcriptomics-1.html)
+
+
+
diff --git a/manuscript/15-Chromatin-Methods-Overview.md b/manuscript/15-Chromatin-Methods-Overview.md
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+# 15 Chromatin Methods Overview
+
+{type: iframe, title:15 Chromatin Methods Overview, width:800, height:600, poster:resources/chapt_screen_images/chromatin-methods-overview.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/chromatin-methods-overview.html)
+
+
+
diff --git a/manuscript/16-ATAC-Seq.md b/manuscript/16-ATAC-Seq.md
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+# 16 ATAC-Seq
+
+{type: iframe, title:16 ATAC-Seq, width:800, height:600, poster:resources/chapt_screen_images/atac-seq-1.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/atac-seq-1.html)
+
+
+
diff --git a/manuscript/17-Single-cell-ATAC-Seq.md b/manuscript/17-Single-cell-ATAC-Seq.md
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+# 17 Single cell ATAC-Seq
+
+{type: iframe, title:17 Single cell ATAC-Seq, width:800, height:600, poster:resources/chapt_screen_images/single-cell-atac-seq-1.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/single-cell-atac-seq-1.html)
+
+
+
diff --git a/manuscript/18-ChIP-Seq.md b/manuscript/18-ChIP-Seq.md
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+# 18 ChIP-Seq
+
+{type: iframe, title:18 ChIP-Seq, width:800, height:600, poster:resources/chapt_screen_images/chip-seq-1.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/chip-seq-1.html)
+
+
+
diff --git a/manuscript/19-CUT&RUN-and-CUT&Tag.md b/manuscript/19-CUT&RUN-and-CUT&Tag.md
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+# 19 CUT&RUN and CUT&Tag
+
+{type: iframe, title:19 CUT&RUN and CUT&Tag, width:800, height:600, poster:resources/chapt_screen_images/cutrun-and-cuttag.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/cutrun-and-cuttag.html)
+
+
+
diff --git a/manuscript/2-A-Very-General-Genomics-Overview.md b/manuscript/2-A-Very-General-Genomics-Overview.md
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+# 2 A Very General Genomics Overview
+
+{type: iframe, title:2 A Very General Genomics Overview, width:800, height:600, poster:resources/chapt_screen_images/a-very-general-genomics-overview.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/a-very-general-genomics-overview.html)
+
+
+
diff --git a/manuscript/20-DNA-Methylation-Sequencing.md b/manuscript/20-DNA-Methylation-Sequencing.md
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+# 20 DNA Methylation Sequencing
+
+{type: iframe, title:20 DNA Methylation Sequencing, width:800, height:600, poster:resources/chapt_screen_images/dna-methylation-sequencing.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/dna-methylation-sequencing.html)
+
+
+
diff --git a/manuscript/21-Microbiome-Sequencing.md b/manuscript/21-Microbiome-Sequencing.md
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+# 21 Microbiome Sequencing
+
+{type: iframe, title:21 Microbiome Sequencing, width:800, height:600, poster:resources/chapt_screen_images/microbiome-sequencing.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/microbiome-sequencing.html)
+
+
+
diff --git a/manuscript/22-ITCR--omic-Tool-Glossary.md b/manuscript/22-ITCR--omic-Tool-Glossary.md
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+# 22 ITCR -omic Tool Glossary
+
+{type: iframe, title:22 ITCR -omic Tool Glossary, width:800, height:600, poster:resources/chapt_screen_images/itcr--omic-tool-glossary.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/itcr--omic-tool-glossary.html)
+
+
+
diff --git a/manuscript/3-Guidelines-for-Good-Metadata.md b/manuscript/3-Guidelines-for-Good-Metadata.md
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+# 3 Guidelines for Good Metadata
+
+{type: iframe, title:3 Guidelines for Good Metadata, width:800, height:600, poster:resources/chapt_screen_images/guidelines-for-good-metadata.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/guidelines-for-good-metadata.html)
+
+
+
diff --git a/manuscript/4-Considerations-for-choosing-tools.md b/manuscript/4-Considerations-for-choosing-tools.md
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+# 4 Considerations for choosing tools
+
+{type: iframe, title:4 Considerations for choosing tools, width:800, height:600, poster:resources/chapt_screen_images/considerations-for-choosing-tools.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/considerations-for-choosing-tools.html)
+
+
+
diff --git a/manuscript/5-General-Data-Analysis-Tools.md b/manuscript/5-General-Data-Analysis-Tools.md
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+# 5 General Data Analysis Tools
+
+{type: iframe, title:5 General Data Analysis Tools, width:800, height:600, poster:resources/chapt_screen_images/general-data-analysis-tools.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/general-data-analysis-tools.html)
+
+
+
diff --git a/manuscript/6-Sequencing-Data.md b/manuscript/6-Sequencing-Data.md
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+# 6 Sequencing Data
+
+{type: iframe, title:6 Sequencing Data, width:800, height:600, poster:resources/chapt_screen_images/sequencing-data.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/sequencing-data.html)
+
+
+
diff --git a/manuscript/7-Microarray-Data.md b/manuscript/7-Microarray-Data.md
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+# 7 Microarray Data
+
+{type: iframe, title:7 Microarray Data, width:800, height:600, poster:resources/chapt_screen_images/microarray-data.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/microarray-data.html)
+
+
+
diff --git a/manuscript/8-Annotating-Genomes.md b/manuscript/8-Annotating-Genomes.md
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+# 8 Annotating Genomes
+
+{type: iframe, title:8 Annotating Genomes, width:800, height:600, poster:resources/chapt_screen_images/annotating-genomes.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/annotating-genomes.html)
+
+
+
diff --git a/manuscript/9-DNA-Methods-Overview.md b/manuscript/9-DNA-Methods-Overview.md
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+# 9 DNA Methods Overview
+
+{type: iframe, title:9 DNA Methods Overview, width:800, height:600, poster:resources/chapt_screen_images/dna-methods-overview.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/dna-methods-overview.html)
+
+
+
diff --git a/manuscript/About-the-Authors.md b/manuscript/About-the-Authors.md
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+# About the Authors
+
+{type: iframe, title:About the Authors, width:800, height:600, poster:resources/chapt_screen_images/about-the-authors.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/about-the-authors.html)
+
+
+
diff --git a/manuscript/About-this-Course.md b/manuscript/About-this-Course.md
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+# About this Course
+
+{type: iframe, title:About this Course, width:800, height:600, poster:resources/chapt_screen_images/index.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/index.html)
+
+
+
diff --git a/manuscript/Book.txt b/manuscript/Book.txt
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+1-Introduction.md
+2-A-Very-General-Genomics-Overview.md
+3-Guidelines-for-Good-Metadata.md
+4-Considerations-for-choosing-tools.md
+5-General-Data-Analysis-Tools.md
+6-Sequencing-Data.md
+7-Microarray-Data.md
+8-Annotating-Genomes.md
+9-DNA-Methods-Overview.md
+10-Whole-Genome-or-Exome-Sequencing.md
+11-RNA-Methods-Overview.md
+12-Bulk-RNA-seq.md
+13-Single-cell-RNA-seq.md
+14-Spatial-transcriptomics.md
+15-Chromatin-Methods-Overview.md
+16-ATAC-Seq.md
+17-Single-cell-ATAC-Seq.md
+18-ChIP-Seq.md
+19-CUT&RUN-and-CUT&Tag.md
+20-DNA-Methylation-Sequencing.md
+21-Microbiome-Sequencing.md
+22-ITCR--omic-Tool-Glossary.md
+About-this-Course.md
+About-the-Authors.md
+References.md
diff --git a/manuscript/References.md b/manuscript/References.md
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+# References
+
+{type: iframe, title:References, width:800, height:600, poster:resources/chapt_screen_images/references.png}
+![](https://hutchdatascience.org/Choosing_Genomics_Tools/references.html)
+
+
+
diff --git a/manuscript/resources/chapt_screen_images/a-very-general-genomics-overview.png b/manuscript/resources/chapt_screen_images/a-very-general-genomics-overview.png
diff --git a/manuscript/resources/chapt_screen_images/about-the-authors.png b/manuscript/resources/chapt_screen_images/about-the-authors.png
diff --git a/manuscript/resources/chapt_screen_images/annotating-genomes.png b/manuscript/resources/chapt_screen_images/annotating-genomes.png
diff --git a/manuscript/resources/chapt_screen_images/atac-seq-1.png b/manuscript/resources/chapt_screen_images/atac-seq-1.png
diff --git a/manuscript/resources/chapt_screen_images/bulk-rna-seq-1.png b/manuscript/resources/chapt_screen_images/bulk-rna-seq-1.png
diff --git a/manuscript/resources/chapt_screen_images/chip-seq-1.png b/manuscript/resources/chapt_screen_images/chip-seq-1.png
diff --git a/manuscript/resources/chapt_screen_images/chromatin-methods-overview.png b/manuscript/resources/chapt_screen_images/chromatin-methods-overview.png
diff --git a/manuscript/resources/chapt_screen_images/considerations-for-choosing-tools.png b/manuscript/resources/chapt_screen_images/considerations-for-choosing-tools.png
diff --git a/manuscript/resources/chapt_screen_images/cutrun-and-cuttag.png b/manuscript/resources/chapt_screen_images/cutrun-and-cuttag.png
diff --git a/manuscript/resources/chapt_screen_images/dna-methods-overview.png b/manuscript/resources/chapt_screen_images/dna-methods-overview.png
diff --git a/manuscript/resources/chapt_screen_images/dna-methylation-sequencing.png b/manuscript/resources/chapt_screen_images/dna-methylation-sequencing.png
diff --git a/manuscript/resources/chapt_screen_images/general-data-analysis-tools.png b/manuscript/resources/chapt_screen_images/general-data-analysis-tools.png
diff --git a/manuscript/resources/chapt_screen_images/guidelines-for-good-metadata.png b/manuscript/resources/chapt_screen_images/guidelines-for-good-metadata.png
diff --git a/manuscript/resources/chapt_screen_images/index.png b/manuscript/resources/chapt_screen_images/index.png
diff --git a/manuscript/resources/chapt_screen_images/introduction.png b/manuscript/resources/chapt_screen_images/introduction.png
diff --git a/manuscript/resources/chapt_screen_images/itcr--omic-tool-glossary.png b/manuscript/resources/chapt_screen_images/itcr--omic-tool-glossary.png
diff --git a/manuscript/resources/chapt_screen_images/microarray-data.png b/manuscript/resources/chapt_screen_images/microarray-data.png
diff --git a/manuscript/resources/chapt_screen_images/microbiome-sequencing.png b/manuscript/resources/chapt_screen_images/microbiome-sequencing.png
diff --git a/manuscript/resources/chapt_screen_images/references.png b/manuscript/resources/chapt_screen_images/references.png
diff --git a/manuscript/resources/chapt_screen_images/rna-methods-overview.png b/manuscript/resources/chapt_screen_images/rna-methods-overview.png
diff --git a/manuscript/resources/chapt_screen_images/sequencing-data.png b/manuscript/resources/chapt_screen_images/sequencing-data.png
diff --git a/manuscript/resources/chapt_screen_images/single-cell-atac-seq-1.png b/manuscript/resources/chapt_screen_images/single-cell-atac-seq-1.png
diff --git a/manuscript/resources/chapt_screen_images/single-cell-rna-seq.png b/manuscript/resources/chapt_screen_images/single-cell-rna-seq.png
diff --git a/manuscript/resources/chapt_screen_images/spatial-transcriptomics-1.png b/manuscript/resources/chapt_screen_images/spatial-transcriptomics-1.png
diff --git a/manuscript/resources/chapt_screen_images/whole-genome-or-exome-sequencing.png b/manuscript/resources/chapt_screen_images/whole-genome-or-exome-sequencing.png