Umap and Bismap: quantifying genome and methylome mappability

Nucleic Acids Research
Mehran KarimzadehMichael M Hoffman

Abstract

Short-read sequencing enables assessment of genetic and biochemical traits of individual genomic regions, such as the location of genetic variation, protein binding and chemical modifications. Every region in a genome assembly has a property called 'mappability', which measures the extent to which it can be uniquely mapped by sequence reads. In regions of lower mappability, estimates of genomic and epigenomic characteristics from sequencing assays are less reliable. These regions have increased susceptibility to spurious mapping from reads from other regions of the genome with sequencing errors or unexpected genetic variation. Bisulfite sequencing approaches used to identify DNA methylation exacerbate these problems by introducing large numbers of reads that map to multiple regions. Both to correct assumptions of uniformity in downstream analysis and to identify regions where the analysis is less reliable, it is necessary to know the mappability of both ordinary and bisulfite-converted genomes. We introduce the Umap software for identifying uniquely mappable regions of any genome. Its Bismap extension identifies mappability of the bisulfite-converted genome. A Umap and Bismap track hub for human genome assemblies GRCh37/hg19 an...Continue Reading

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Citations

Mar 7, 2019·Genes·Phoebe Oldach, Conrad A Nieduszynski
Apr 5, 2020·Bioinformatics·Christopher PockrandtKnut Reinert
Jul 21, 2020·PLoS Computational Biology·David R Kelley
Jun 30, 2019·Scientific Reports·Haley M AmemiyaAlan P Boyle
Mar 20, 2021·Science·Sara BizzottoChristopher A Walsh
Sep 8, 2021·Frontiers in Cell and Developmental Biology·Oza ZaheedKellie Dean

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Datasets Mentioned

BETA
SRR1946819
SRR1946820
ENCSR000EHH

Methods Mentioned

BETA
ChIP-seq
RRBS
array technologies

Software Mentioned

Bismap
BWA
DiseaseMeth
bigWig
Ensembl
MACS2
Bismark
BEADS
BSmooth
mappability

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