| This tool is part of the CloudMap pipeline for analysis of mutant genome sequences. For further details, please see Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)
The polymorphic Hawaiian strain CB4856 is used as a mapping strain in most cases but in principle any sequenced nematode strain that is significantly different from the mutant strain can be used for mapping. The tool plots the ratio of mapping strain (Hawaiian)/mutant strain (N2) nucleotides at all SNP positions, reflecting the number of recombinants in the sequenced pool of animals. Chromosomes which contain regions of linkage to the causal mutation will have regions where the ratio of mapping strain (Hawaiian)/total reads will be equal to 0. The scatter plots for such linked regions will have a high number of data points lying exactly on the X axis. A loess regression line is plotted through all the points on a given chromosome giving further accuracy to the linked region. Each scatter plot has a corresponding frequency plot that displays regions of linked chromosomes where pure parental (mutant strain) alleles are concentrated. 1Mb bins for the 0 ratio SNP positions are colored gray by default and .5Mb bins are colored in red. By default, frequency plots of pure parental alleles are normalized to remove false linkage caused by previously described (Seidel et al. 2008) patterns of genetic incompatibility between Bristol and Hawaiian strains. This normalization can be turned off via a checkbox input form setting. The experimental design required to generate data for the plots is described in the CloudMap paper (Fig.6A): |
hg clone https://toolshed.g2.bx.psu.edu/repos/gregory-minevich/snp_mapping_using_wgs
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Map a mutation by plotting recombination frequencies resulting from crossing to a highly polymorphic strain | 1.0.0 | any | |