Phaster Alignment Track Settings
 
Phaster Alignments   (All Alignments tracks)

Display mode:   

Display read names
Attempt to join paired end reads by name
Minimum alignment quality:

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query

Additional coloring modes:
Color by strand (blue for +, red for -)
Use gray for
Use R,G,B colors specified in user-defined tag
No additional coloring

Display data as a density graph:

BAM configuration help

View table schema

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generated using the Princeton dataset to the CB4856 reference genome with the alignment algorithm phaster (P. Green, unpublished).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.