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Description
A resource of 49 recombinant CB4856/N2 inbred lines (RILs) and 60 introgression lines (ILs) was recently sequenced with SOLiD technology by the University of Liverpool. This track displays the coverage depth of the REAPR-processed JR-Assembler contigs from CB4856, the control Hawaiian strain for this experiment.
Display Conventions and Configuration
Coverage depth is displayed in WIG format. The mean coverage depth of this strain, aligned to the de novo contigs, is 11.5598x: the default vertical viewing range has been set to this height to allow for normalized visualization of specific regions across many different RILs/ILs with different coverage. These parameters can be adjusted as desired in the Track Settings.
Methods
RIL and IL strains developed in the Kammenga lab (See Li 2006 and Doroszuk 2009), as well as this CB4856 control, were sequenced at the University of Liverpool with Applied Biosystems SOLiD 4, and aligned to the REAPR-processed JR-Assembly contigs in colorspace with bwa-0.5.9 (setting the edit distance to 6 with -n). Base-by-base coverage data was extracted using samtools mpileup and converted into WIG format for the purpose of browser display.
Credits
Please feel free to contact Owen Thompson with any questions and/or concerns regarding this or other tracks.
Sequence data from this strain is not currently available from the Short Read Archive, but may be made available upon request to the or Waterston labs. A visual representation of the behavior of CB4856 SNVs in this control sample is available for download here.
Thanks to the Kammenga lab for their work generating the RIL/IL resource, and to Dr. Cossins at the University of Liverpool for generating the sequencing data.
Thanks to Heng Li and Richard Durbin for their work developing BWA and samtools.
References
Li Y, Alvarez OA, Gutteling EW, et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. 2006;2(12):e222. PMID 17196041.
Doroszuk A, Snoek LB, Fradin E, Riksen J, Kammenga J. A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans. Nucleic Acids Res. 2009;37(16):e110. PMID 19542186.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-60. PMID 19451168.
Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9. PMID 19505943.
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