在颜色或NR优化核苷酸的空间位置特异性甲基化参数估计

FadE FadE is a software package which was designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms. Usage FadE attempts to estimate the methylation rate directly in color or nucleotide space. FadE requires an alignment file and a reference file and builds an index file from which methylation rates are determined. If present FadE can also incorporate control and treatment files to better infer error rates and increase accuracy. The most common use of FadE can be run using: ./FadE methcall alignment.idx > methylation_results.txt Algorithm and Performance FadE uses an iterative optimization strategy to determine the methylation rate at each site in the methylome. Such a strategy allows FadE to provide more accurate results than other algor

fade.0.0.2
sampleData
fade_manual.pdf
src