> For the complete documentation index, see [llms.txt](https://book.ncrnalab.org/teaching/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses.md).

# Part III. NGS DATA ANALYSES

- [1.Mapping](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/1.mapping.md)
- [1.1 Genome Browser](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/1.mapping/1.1-genome-browser.md)
- [1.2 bedtools and samtools](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/1.mapping/1.2-bedtools-samtools.md)
- [2.RNA-seq](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/2.rna-seq.md)
- [2.1.Expression Matrix](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/2.rna-seq/2.1.expression-matrix.md)
- [2.2.Differential Expression with Cufflinks](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/2.rna-seq/2.2.differential-expression-with-cufflinks.md)
- [2.3.Differential Expression with DEseq2 and edgeR](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/2.rna-seq/2.3.differential_expression_with_deseq2-edger.md)
- [3.ChIP-seq](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/3.chip-seq.md)
- [4.Motif](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/4.motif.md)
- [4.1.Sequence Motif](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/4.motif/sequence_motif.md)
- [4.2.Structure Motif](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/4.motif/structure_motif.md)
- [5.RNA Network](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/5.rna-network.md)
- [5.1.Co-expression Network](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/5.rna-network/co_expression.md)
- [5.2.miRNA Targets](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/5.rna-network/mirna-targets.md)
- [5.3. CLIP-seq (RNA-Protein Interaction)](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/5.rna-network/clip-seq.md)
- [6.RNA Regulation - I](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation.md)
- [6.1.Alternative Splicing](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/alternative-splicing.md)
- [6.2.APA (Alternative Polyadenylation)](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/apa.md)
- [6.3.Chimeric RNA](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/chimeric.md)
- [6.4.RNA Editing](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/rna_editing.md)
- [6.5.SNV/INDEL](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/snv_rna-seq.md)
- [7.RNA Regulation - II](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/7.rna-regulation-ii.md)
- [7.1.Translation: Ribo-seq](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/7.rna-regulation-ii/ribo_seq.md)
- [7.2.RNA Structure](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/7.rna-regulation-ii/structure.md)
- [8.cfDNA](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/8.cfdna.md)
- [8.1.Basic cfDNA-seq Analyses](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/8.cfdna/8.1.basic-cfdna-seq-analyses.md)