The Uniqueome: A mappability resource for short-tag sequencing

Ryan Koehler, Hadar Issac, Nicole Cloonan*, and Sean M Grimmond

*Address correspondence to: n.cloonan@uq.edu.au

BioInformatics, Oxford Press

Abstract

Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here we present the "uniqueome", a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data is available for human, mouse, fly, and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data.

Supplementary Material

Supplementary Methods. [Click Here]
Supplementary Figure 1. Schematic illustrating the effect of sequencing error on uniquely mapping tags. [Click Here]
Supplementary Figure 2. IGV screen shot of mismapping pairs. [Click Here]
Supplementary Table 1. Proportions of unique start-sites for color-space short tag alignments. [Click Here]
Supplementary Table 2. Proportions of coverage for nucleotide-space short tag alignments. [Click Here]
Supplementary Table 3. Proportions of coverage for color-space short tag alignments. [Click Here]
Supplementary Table 4. Proportions of unique start sites and genome coverage (by any unique tag) for nucleotide-space short tag alignments in hg19. [Click Here]
Supplementary Table 5. Proportions of unique start sites and genome coverage (by any unique tag) for nucleotide-space short tag alignments in hg19 RefSeq exon-exon junctions. [Click Here]
Supplementary Table 6. Proportions of unique start sites and genome coverage (by any unique tag) for color-space short tag alignments in hg19 RefSeq exon-exon junctions. [Click Here]
Supplementary File 1. PDF tutorial on using uniqueome files with Galaxy. [Click Here]
Supplementary File 2. PDF tutorial on using ISAS to generate custom uniqueomes. [Click Here]
Supplementary File 3. A tarball containing the scripts used to manipulate ISAS output. [Click Here]
Downloads. Repository of BED, bigBed, Wig, and bigWig files. [Click Here] Note: additional files can be downloaded from Univeristy of Queensland, Australia