Genome Feature
This track represents the genome features in an abstract way.
Display Conventions and Configuration
The colors used for each of the genome feature represents:
- - Tel, Telomeric sequence
- - 45S, 45S within the rDNA unit sequence
- - Gap, N-base sequence gaps
- - Cen, Centromere with kinetochore support
- - PAR, PAR region
Methods
- Telomeres have been identified with
seqtk telo -d 10000.
- 45S units have been extracted from KY962518.1 and queried gainst each assembly using MashMap3 with
mashmap -t $CPU --noSplit -q human_45S.fa -r $asm.fa -s 13332 --pi 85 -f none -o $sp_ver.45S.mashmap.out and converted to bed format.
- Gaps have been identified with
seqtk gap.
- Centromeres with kinetochore support have been identified using methylation data and CENP-A CUT&RUN.
- PAR region identified in the v1-v1.1 XY assemblies (Makova et al., bioRxiv, 2023) have been aligned using
minimap2 -asm10 to the v2 assemblies. Then, UCSC Toolkit (axtChain and liftOver) have been used to liftover the coordinates. For the bonobo genome (mPanPan1), the PAR sequences were extracted from the v1 assemblies and mapped using minimap2. To verify the accuracy of the PAR boundaries, PARs from the X chromosome were extracted and mapped to the Y chromosome using minimap2.
Notes
Centromere methods will be updated soon.
Credits
- Arang Rhie, National Human Genome Research Institute, National Institutes of Health
- Centromere: Glennis Logsdon, University of Pennsylvania;
Fedor Ryabov, National Research University Higher School of Economics, Moscow, Russia; and
Ivan A. Alexandrov, Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Israel
- PAR: Qiuhui Li
Reference