Whole-Genome Bisulfite Sequencing on Illumina
Corresponding Organization :
Other organizations : Kyushu University, Tokyo University of Agriculture, The University of Tokyo, Tohoku University
Protocol cited in 15 other protocols
Variable analysis
- Sequencing platform (Illumina HiSeq 2000)
- Sequenced reads
- Alignment to reference genome (mouse mm9)
- Bisulfite conversion rate
- CG methylation levels
- Non-CG methylation levels
- Sequencing read length (100 nucleotides)
- Sequencing mode (single-ended)
- Sequencing coverage (3x10^8 copies per lane)
- Number of mismatches allowed in alignment (maximum of 2)
- Minimum coverage threshold for CG sites (6x) and non-CG sites (4x)
- Maximum coverage threshold for cytosines (100x)
- Reference genome (mouse mm9)
- Lambda phage genome for estimating bisulfite conversion rate
- Reads that uniquely aligned to the lambda phage genome to estimate bisulfite conversion rate
Annotations
Based on most similar protocols
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