Description
This track displays sam/bam alignments generated using the Princeton dataset to the CB4856 reference genome with the alignment algorithm phaster (P. Green, unpublished).
Display Conventions and Configuration
Alignments are displayed in bam format. Because of the density of this information the default display mode on the browser is set to "dense"; if there is a region of interest it is recommended that users switch to "squish" without read names displayed. By default paired end reads are joined and alignments are greyscaled according to mapping quality.
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. Bam files were merged, indexed, and uploaded without alteration.
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 generating the SAM/BAM format.
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.
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