Description: minor spelling issues Author: Sascha Steinbiss Author: Étienne Mollier Bug: https://github.com/PacificBiosciences/kineticsTools/pull/73 Last-Update: 2020-04-20 Index: kineticstools/doc/manual.rst =================================================================== --- kineticstools.orig/doc/manual.rst +++ kineticstools/doc/manual.rst @@ -31,7 +27,7 @@ The basic mode of kineticsTools does an Modifications Identification ---------------------------- kineticsTools also has a *Modification Identification* mode that can decode multi-site IPD 'fingerprints' into a reduced set of calls of specific modifications. This feature has the following benefits: - * Different modifications occuring on the same base can be distinguished (for example m5C and m4C) + * Different modifications occurring on the same base can be distinguished (for example m5C and m4C) * The signal from one modification is combined into one statistic, improving sensitivity, removing extra peaks, and correctly centering the call OPTIONS @@ -52,7 +48,7 @@ Filtering and Trimming kineticsTools uses the Mapping QV generated by BLASR or pbmm2 and stored in the alignments or BAM file (or AlignmentSet) to ignore reads that aren't confidently mapped. The default minimum Mapping QV required is 10, implying that BLASR has :math:`90\%` confidence that the read is correctly mapped. Because of the range of readlengths inherent in PacBio dataThis can be changed in using the --mapQvThreshold command line argument, or via the SMRTPortal configuration dialog for Modification Detection. -There are a few features of PacBio data that require special attention in order to acheive good modification detection performance. +There are a few features of PacBio data that require special attention in order to achieve good modification detection performance. kineticsTools inspects the alignment between the observed bases and the reference sequence -- in order for an IPD measurement to be included in the analysis, the PacBio read sequence must match the reference sequence for :math:`k` around the cognate base. In the current module :math:`k=1` The IPD distribution at some locus be thought of as a mixture between the 'normal' incorporation process IPD, which is sensitive to the local sequence context and DNA modifications and a contaminating 'pause' process IPD which have a much longer duration (mean >10x longer than normal), but happen rarely (~1% of IPDs). Note: Our current understanding is that pauses do not carry useful information about the methylation state of the DNA, however a more careful analysis may be warranted. Also note that modifications that drastically increase the