Description

This track displays the coverage depth generated by aligning raw Illumina reads from the Princeton dataset to the CB4856 reference genome using the alignment algorithm phaster (P. Green, unpublished).

Display Conventions and Configuration

Coverage depth is displayed in WIG format. The mean coverage depth of the Princeton dataset aligned to the CB4856 reference is approximately 70x: the default vertical viewing range has been set to 200x to allow for visualization of regions of greater depth without auto-scaling in repetitive regions. These parameters can be adjusted as desired in the Track Settings.

Methods

Raw paired-end Illumina reads were converted to calf format and aligned to the reference genome. A maximum gapped indel size of 300bp was allowed as in the Million Mutation Project, and coverage depth was extracted from the merged bam file using the samtools "mpileup" command.

Credits

Please feel free to contact Owen Thompson with any questions and/or concerns regarding this or other tracks.

The raw data used to generate the depth of coverage displayed here is available from the Short Read Archive as experiment SRX1001806.

Many thanks to Phil Green for his alignment algorithm phaster, and to Heng Li for his work creating samtools.

References

Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9. PMID 19505943.

Thompson O, Edgley M, Strasbourger P, et al. The million mutation project: a new approach to genetics in Caenorhabditis elegans. Genome Res. 2013;23(10):1749-62. PMID 23800452.