Table 5 Notation table
From: An effective method to resolve ambiguous bisulfite-treated reads
Symbol | Definition |
|---|---|
M | One of the multireads |
G | The reference genome |
\({M}_{k}\) | The k-th base of the multiread M |
\({G}_{s}\) | The s-th base of the reference genome G |
\({U}_{lt}\) | The t-th base on the l-th overlapped unique reads |
\({S}_{j}\) | Probability of M aligned to the j-th position of G |
\({{\varepsilon }_{k}}\) | Probability of sequencing errors in \({M}_{k}\) |
\({{\varepsilon }_{lt}}\) | Probability of sequencing errors in \({U}_{lt}\) |
loss | A global loss function |
WinLen | The certain length we defined |
a[i] | Actual coverage of every locus in WinLen |
\(\overline{x}\) | The average depth of coverage from 0 to \(WinLen-1\) |
\({S}_{{{M}_{k}}{{G}_{s}}}\) | Probability of aligning \({M}_{k}\) to \({G}_{s}\), related to the base \({M}_{k}\) and \({G}_{s}\) |
\(P({{M}_{k}},{{G}_{s}})\) | Part of \({S}_{{{M}_{k}}{{G}_{s}}}\). The probability of observing \({M}_{k}\) for a given base \({G}_{s}\) |
\(Score({{M}_{k}},{{G}_{s}})\) | Part of \({S}_{{{M}_{k}}{{G}_{s}}}\). A similar score between \({M}_{k}\) and \({G}_{s}\) |
\(S[{{G}_{s}}]\) | Total similar score when the base of the reference genome is \({G}_{s}\) |
\({S}_{{{M}_{k}}{{U}_{t}}}\) | Probability of aligning \({M}_{k}\) to the l-th overlapping unique reads \({{U}_{t}}\) |
\({S}_{{{M}_{k}}{{U}_{lt}}}\) | Probability of aligning \({M}_{k}\) to all overlapping unique reads \({{U}_{lt}}\) |
\(P({{M}_{k}} \rightarrow {{U}_{lt}})\) | Probability of no sequencing errors occurring in both \({M}_{k}\) and \({{U}_{lt}}\) |
\(Score({{M}_{k}},{{U}_{lt}})\) | Part of \(P({{M}_{k}} \rightarrow {{U}_{lt}})\). A similar score between \({M}_{k}\) and \({{U}_{lt}}\) |