MOTIVATION: 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. At best, sequencing assays will produce misleadingly low numbers of reads in these regions. At worst, 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. While many tools consider mappability during the read mapping process, subsequent analysis often loses this information. 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. RESULTS: We introduce the Umap software for identifying uniquely mappable regions of any genome. Its Bismap extension identifies mappability of the bisulfite-converted genome. With a read length of 24 bp, 18.7% of the unmodified genome and 33.5% of the bisulfite-converted genome is not uniquely mappable. This complicates interpretation of functional genomics experiments using short-read sequencing, especially in regulatory regions. For example, 81% of human CpG islands overlap with regions that are not uniquely mappable. Similarly, in some ENCODE ChIP-seq datasets, up to 50% of peaks overlap with regions that are not uniquely mappable. We also explored differentially methylated regions from a case-control study and identified regions that were not uniquely mappable. In the widely used 450K methylation array, 4,230 probes are not uniquely mappable. Genome mappability is higher with longer sequencing reads, but most publicly available ChIP-seq and reduced representation bisulfite sequencing datasets have shorter reads. Therefore, uneven and low mappability remains a concern in a majority of existing data. AVAILABILITY: A Umap and Bismap track hub for human genome assemblies GRCh37/hg19 and GRCh38/hg38, and mouse assemblies GRCm37/mm9 and GRCm38/mm10 is available at http://bismap.hoffmanlab.org for use with the UCSC and Ensembl genome browsers. We have deposited in Zenodo the current version of our software (https://doi.org/10.5281/zenodo.800648) and the mappability data used in this project (https://doi.org/10.5281/zenodo.800645). In addition, the software (https://bitbucket.org/hoffmanlab/umap) is freely available under the GNU General Public License, version 3 (GPLv3).
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