Smalt Depth Track Settings
 
Smalt Alignment Depth   (All Alignments tracks)

Display mode:   

Type of graph:
Track height: pixels (range: 11 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 200)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
View table schema

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 SMALT (see references).

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 aligned to the reference genome using SMALT version 0.7.0.1 with default settings. 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 to Hannes Ponstingl for his alignment algorithm SMALT, and to Heng Li for his work creating samtools.

References

Ponstingl, Hannes. (2012, May 11). SMALT - Sequence Mapping and Alignment Tool. Retrieved from http://www.sanger.ac.uk/resources/software/smalt.

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