Adj NSome Covrg Track Settings
 
Adjusted nucleosome coverage (25bp)   (All Mapping and Sequencing tracks)

Display mode:   

Type of graph:
Track height: pixels (range: 11 to 100)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: -11.93 to 8.76)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
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Data coordinates converted via liftOver from: Jan. 2007 (WS170/ce4)
Data last updated at UCSC: 2008-09-30

Methods

The plot represents relative mononucleosome enrichment at each position in the genome (on a log of 2 scale). The coverage metric is given according to a formula [ (1+n)/N ] / [ (1+c)/C ] where n and c are the numbers of putative 147 base pair cores covering each base pair from nucleosome and control data, N and C are the total number of nucleosome and control reads obtained by SOLiD sequencing with 25 base pairs mapped to the reference genome.

Data download

The source data for this track can be fetched from our ftp server (nucleosomeAdjustedCoverage.wigAscii.gz; 450 Mb compressed, 1.6 Gb uncompressed).
This data is formatted into the two-column variableStep wiggle format.

Credits

The data for this track is supplied by the Sidow Lab and the Fire Lab at the Stanford School of Medicine.
Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering.

References

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. PMID: 18477713; PMC: PMC2493394

Supported oligo ligation detection (SOLiD) sequencing technology from Applied Biosystems.