Umap S24 Track Settings
 
Single-read mappability with 24-mers   (Umap)

This track is part of a parent called Umap. To show other tracks of this parent, go to the Umap configuration page.

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Data last updated: 2020-02-25 10:48:17

Umap Trackhub

Umap: Unique mappability of the genome

Description

These tracks indicate regions with uniquely mappable reads of particular lengths.

Umap single-read mappability

  • Umap S24: Uniquely mappable regions with a read length of 24 nucleotides
  • Umap S36: Uniquely mappable regions with a read length of 36 nucleotides
  • Umap S50: Uniquely mappable regions with a read length of 50 nucleotides
  • Umap S100: Uniquely mappable regions with a read length of 100 nucleotides

Umap multi-read mappability

  • Umap M24: Multi-read mappability with a read length of 24 nucleotides
  • Umap M36: Multi-read mappability with a read length of 36 nucleotides
  • Umap M50: Multi-read mappability with a read length of 50 nucleotides
  • Umap M100: Multi-read mappability with a read length of 100 nucleotides

You can use these tracks for many purposes including filtering unreliable signal from sequencing assays.

Umap single-read mappability tracks mark any region of the genome that is uniquely mappable by at least one k-mer. To calculate the single-read mappability, you must find the overlap of a given region with this track. Umap multi-read mappability tracks represent the probability that a randomly selected k-mer which overlaps with a given position is uniquely mappable.

For greater detail and explanatory diagrams, see the preprint, the Umap and Bismap project website , or the Umap and Bismap software documentation.

Track format

Single-read mappability tracks: bigBed 6-column format

Multi-read mappability tracks: bigWig

These tracks are available for m9/GRCm37, mm10/GRCm38, hg19/GRCh37 and hg38/GRCh38 genome assemblies.

Credits

Anshul Kundaje (Stanford university) created the original Umap software in MATLAB. Mehran Karimzadeh (Michael Hoffman lab, Princess Margaret Cancer Centre) implemented the Python version of Umap and added features, including Bismap.

Contact, support and questions

Please ask your questions about the Umap software and this track hub using the Umap and Bismap mailing list. To report a bug or request, please use the Umap and Bismap issue tracker.