Bismap: Unique mappability of the bisulfite converted genomes

Description

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

Bismap single-read mappability

• Bismap S24 +: Uniquely mappable regions of the bisulfite converted genome with a read length of 24 nucleotides on the forward strand
• Bismap S24 -: Uniquely mappable regions of the bisulfite converted genome with a read length of 24 nucleotides on the reverse strand
• Bismap S36 +: Uniquely mappable regions of the bisulfite converted genome with a read length of 36 nucleotides on the forward strand
• Bismap S36 -: Uniquely mappable regions of the bisulfite converted genome with a read length of 36 nucleotides on the reverse strand
• Bismap S50 +: Uniquely mappable regions of the bisulfite converted genome with a read length of 50 nucleotides on the forward strand
• Bismap S50 -: Uniquely mappable regions of the bisulfite converted genome with a read length of 50 nucleotides on the reverse strand
• Bismap S100 +: Uniquely mappable regions of the bisulfite converted genome with a read length of 100 nucleotides on the forward strand
• Bismap S100 -: Uniquely mappable regions of the bisulfite converted genome with a read length of 100 nucleotides on the reverse strand

Bismap multi-read mappability

• Bismap M24: Multi-read mappability of the bisulfite converted genome with a read length of 24 nucleotides
• Bismap M36: Multi-read mappability of the bisulfite converted genome with a read length of 36 nucleotides
• Bismap M50: Multi-read mappability of the bisulfite converted genome with a read length of 50 nucleotides
• Bismap M100: Multi-read mappability of the bisulfite converted genome with a read length of 100 nucleotides

You can use these tracks for many purposes, including filtering unreliable signal from sequencing assays involving bisulfite conversion, such as whole-genome bisulfite sequencing or reduced representation bisulfite sequencing.

Bismap single-read mappability tracks mark any region of the bisulfite-converted genome that is uniquely mappable by at least one k-mer on the specified strand. We generated the mappability of the forward strand by converting all instances of cytosine to Thymine. Similarly, we generated the mappability of the reverse strand by by converting all instances of guanine to adenine. To calculate the single-read mappability, you must find the overlap of a given region with the region that is uniquely mappable on both strands. Regions not uniquely mappable on both strands or have a low multi-read mappability might bias the downstream analysis. Bismap multi-read mappability tracks represent the probability that a randomly selected k-mer which overlaps with a given position is uniquely mappable. Multi-read mappability track is calculated for k-mers that are uniquely mappable on both strands, and thus there is no strand specification.

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.