Whole Genome Bisulfite Sequencing (WGBS) is a bisulfite sequencing method to detect in-depth DNA methylation across the entire genome, including methylation at CpG sites and less common non-CpG site such as CNG. WGBS is the gold standard for bisulfite based DNA methylation st...
Target bisulfite sequencing designs primers for target fragments, performs PCR amplification after BS conversion, and finally constructs libraries for next-generation sequencing. The sequencing depth of target region sequencing can reach from hundreds to tens of thousands, enabling precise detection of meth...
The clean reads were aligned to the sheep reference genome (Oar_v3.1) and the bisulfite mapping of methylation sites was performed using Bismark software. The duplicates were reads that aligned with the same region of the genome, and can estimated the sequencing depth and coverage. The bisulfite...
An in-depth comparative analysis betweenWhole Genome Bisulfite Sequencing (WGBS)and Reduced Representation Bisulfite Sequencing (RRBS) can elucidate their respective strengths and limitations, assisting researchers in selecting the optimum approach that aligns with their investigative objectives. For instance,...
The results of the bisulfite-sequencing experiments for the genes \\{PDCD5\\} and \\{TIMP2\\} confirmed the methylation status identified by MeDIP-Seq, and the mRNA expression levels of these two genes were consistent with their \\{DNA\\} methylation profiles. To our knowledge, the ...
Through whole genome resequencing, we obtained 3351.4 Gb of data, with an average sequencing depth of 18.23X per individual, genome coverage of 96.66%, and a mapping rate of 99.9%. After strict filtering, we obtained 6,826,208 high-confidence SNPs. In the principal components analysis, the ...
and the sequencing depth should be about half of the average value of autosomes in the female genome reads. Using this method, we identified 306 W-linked scaffolds in the non-PAR region representing a 16.4 Mb length with a scaffold N50 of 128 kb. Considering the interference of W reads and...
In this case, we used QUAL > 30 (quality score from the variant caller, PHRED-scaled) and DP > 10 (sequencing depth at the position, in reads) for quality filtering filtering. Please see the bcftools documentation for more information about filtering options. What we have provided here is ...
Table 2. Summary of sequencing data after bisulfite transformation. 3.2. Analysis of Sequencing Depth and Sulfite Conversion Efficiency Sequencing depth statistics for whole-genome methylation of pituitary tissue are presented in Figure 1A. These data show that the methylation sequencing depth for each...
(b) The distribution of the sequencing depth of the genome and transcriptome. (c) Contigs in HN mapped to the previous CM01 genome. Figure 3. Distribution of m4C and m6A methylated sites in 14 contigs in the HN genome. and Cordyceps subsessilis both contain seven chromosomes. However,...