Microsatellites Track Settings

Microsatellite repeats (All Mapping and Sequencing tracks)

Display mode: Reset to defaults

Type of graph:
Track height:	pixels (range: 11 to 128)
Data view scaling:	Always include zero:
Vertical viewing range:	min:	max: (range: 0 to 127)
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

List subtracks: only selected/visible all
	Hide Configure	GA Microsatellites	GA Microsatellite repeats	Data format
	Hide Configure	TC Microsatellites	TC Microsatellite repeats	Data format
	Hide Configure	GC Microsatellites	GC Microsatellite repeats	Data format
	Hide Configure	AT Microsatellites	AT Microsatellite repeats	Data format

Data schema/format description and download

Assembly: Human Jan. 2022 (T2T CHM13v2.0/hs1)

Description

This track represents % of simple-sequence (2-mer) repeat pattern. Sequences composed of GA/TC/GC/AT bases are counted if one of the bases repeats (e.g. AAAATTTTAAATT are counted as 13 ATs). Patterns are obtained from every non-verlapping 128 bp window. Values displayed are the % of bases forming the specific repeat type, with a maximum value of 100. These sequence patterns are useful for predicting HiFi or ONT coverage biases, as described in Nurk et al. 2022 (Fig. 3) and Mc Cartney et al., 2022.

Display Conventions and Configuration

- GA
- TC
- GC
- AT

Methods

The track was generated using Seqrequester, a Meryl and Canu utility module. The tracks can be generated using seqrequester microsatellite. The code to generate these patterns can be found at T2T-Polish/pattern.

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can also be accessed from scripts through our REST API.

This track is a container of multiple subtracks; the underlying data are stored in bigWig files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tool bigWigToWig, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:

bigWigToWig https://hgdownload.soe.ucsc.edu/gbdb/hs1/microsatellites/chm13v2.0.microsatellite.GA.128.bw -chrom=chr6 -start=0 -end=1000000 stdout

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Release history

2021/05/24, Microsatellite tracks for chm13.v1.0 assembly.
2021/10/13, Microsatellite tracks for chm13.v1.1 assembly.
2022/03/29, Microsatellite tracks for chm13.v2.0 assembly.

Credits

For inquiries, please contact us at Seqrequester or T2T-Polish.

References

Nurk S, Koren S, Rhie A, Rautiainen M et al. The complete sequence of a human genome. Science (2022) doi: 10.1126/science.abj6987
Mc Cartney AM, Shafin K, Alonge M et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat. Methods (2022) doi: 10.1038/s41592-022-01440-3