CrossMap: a versatile tool for coordinate conversion between genome assemblies

Abstract

CrossMap is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://crossmap.sourceforge.net/.

Parallel evolution of male germline epigenetic poising and somatic development in animals

“…73 74 Before turning to the poised state, we first examined the relationships between H3K4me3, 75 H3K27me3, and expression datasets collected from different species. In all species, expression 76 levels were positively correlated with H3K4me3 signal and negatively correlated with 77 H3K27me3 signal, consistent with the known association of these marks with gene activity and 78 repression, respectively (Fig. 1b, Supplementary Fig.…”

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

“…During all comparative analyses, the genomic coordinates of mapped reads, dREG scores, and other parameters of interest were converted to the human assembly (hg19) using CrossMap 52 . We converted genomic coordinates between genome assemblies using reciprocal-best (rbest) nets 53 .…”

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

“…To evaluate differential fractionation in B73 and PH207 following the maize whole-genome duplication, the previously defined B73 Maize1 and Maize2 classifications ) from B73 v2 were converted to B73 v3 coordinates using CrossMap (Zhao et al, 2014), and overlapping gene models were identified. The converted Maize1 and Maize2 classifications were compared with the homologous gene clustering generated using OrthoMCL (Li et al, 2003;Chen et al, 2007) with the B73 version 3.21 and PH207 nucleotide sequences described above.…”