Description
A track showing segmental duplications as generated by
sedef on the assembly: T2T-CHM13-v2.0
Column descriptions can be found here:
columns.
Display Conventions and Configuration
This section describes track configuration controls, or any special display conventions such as the
meaning of different colors in your tracks.
The following colors are used to distinguish levels of similarity:
| less than 90% similarity | Purple |
| 90 - 98% similarity | Light to dark gray |
| 98 - 99% similarity | Yellow |
| greater than 99% similarity | Orange |
Methods
Sedef was run with default parameters on a RepeatMasked genome assembly.
The resulting output (final.bed) was then converted into a browser friendly format (bed9 + extra fields).
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, where the track name is sedefSegDups.
For automated analysis, the data may be downloaded from our
download server as a
bigBed file. The file for this track is called sedefSegDups.bb. Individual regions or the whole
genome annotation can be obtained using our tool bigBedToBed, 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:
bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/hs1/sedefSegDups/sedefSegDups.bb -chrom=chr6 -start=0 -end=1000000 stdout
Please refer to our
mailing
list archives for questions, or our
Data Access FAQ for more
information.
Credits
References
M. R. Vollger et al., Segmental duplications and their variation in a complete
human genome. Science. 2022 April 1; eabj6965. DOI: 10.1126/science.abj6965
Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F.
Fast characterization of segmental duplications in genome assemblies.
Bioinformatics. 2018 Sep 1;34(17):i706-i714.
PMID:
30423092;
PMC:
PMC6129265