Description

This track shows the coverage of read alignments to the genome. BAM files were provided by the data submitters, one or two files per cell. All BAM files for the cells of a cluster were merged and from the result we obtained the coverage, as number of reads per basepair.

Display Conventions and Configuration

For configuration options, see the graph tracks configuration help page.

Methods

The alignments were used as submitted. All BAM files for all cells of a cluster were merged with "samtools merge". From the resulting merged BAM file, coverage was obtained using "wiggletools coverage" and the result was converted with the tool "wigToBigWig".

Data Access

The bigWig files can be downloaded from the track hub directory.

References

Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P. WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. Bioinformatics. 2014 Apr 1;30(7):1008-9. PMID: 24363377; PMC: PMC3967112

The Tabula Muris Consortium, Stephen R. Quake, Tony Wyss-Coray, Spyros DarmanisThe Tabula Muris Consortium, Stephen R. Quake, Tony Wyss-Coray, Spyros Darmanis:
Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris. bioRxiv March 2018, manuscript 237446.