Bisulfite-Seq 해독 생명정보 분석

1. Data filtering: Data filtering includes removing adaptors, contamination and low-quality reads from raw reads.

2. Standard bioinformatics analysis:

1. Reads Alignment (Based on data filtering)

2. Sequence Depth and Coverage Analysis

2.1 Cumulative Distribution of Effective Sequencing Depth in Cytosine

2.2 The Relationship between Genome Coverage and Reads Depth

3. Calculation of Methylation Level

3.1 Averge Methylation Level for C, CG, CHG, and CHH

3.2 Effective Coverage Analysis in Cytosine

4. Global Trends of Methylome

4.1 Proportion of Total Methyl-cytosines, CG, CHG and CHH

4.2 Methylation Level Distribution for CG, CHG and CHH

4.3 Methylation Level of Cytosines (CG, CHG, CHH) for Chromosomes(only for species with complete chromosomes information)

4.4 Methylation Level of Cytosines in Different Genome Regions

4.5 Methylation Level of Cytosines in Different Genomic Elements

4.6 Non-CG Proximal Sequence Features Analysis

5. Genome-wide Methylation Profiling

5.1 Methyl-cytosine Density of Each Chromosome (only for species with complete chromosomes information)

5.2 Methyl-cytosine Density of Each Scaffold (only for speices with incomplete chromosomes information)

5.3 Methylation Heatmap in Different Genomic Features

5.4 DNA Methylation Patterns Across The Transcriptional Units at Whole Genome Level

6. Identification of Differentially Methylated Regions ( DMRs )