Categories
Tag: HiC-Pro
Maternal dominance contributes to subgenome differentiation in allopolyploid fishes
Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article CAS PubMed Google Scholar Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article PubMed Google Scholar Comai, L. The…
Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization
Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….
Genome-wide chromatin interaction map for Trypanosoma cruzi
Johnson, P. J., Kooter, J. M. & Borst, P. Inactivation of transcription by UV irradiation of T. brucei provides evidence for a multicistronic transcription unit including a VSG gene. Cell 51, 273–281 (1987). Article CAS PubMed Google Scholar Matthews, K. R., Tschudi, C. & Ullu, E. A common pyrimidine-rich motif…
Orchestrating Hi-C analysis with Bioconductor
Author(s): Jacques Serizay Affiliation(s): Pasteur Institute, Paris; Institut de Biologie de l’Ecole Normale Supérieure, Paris Hi-C is a chromosome conformation capture experimental method used to comprehensively detect chromatin interactions based on spatial proximity. During the last decade, it has become a prevalent approach in nuclear biology (gene regulation, genome spatial…
Bioconductor – HiCExperiment
DOI: 10.18129/B9.bioc.HiCExperiment Bioconductor class for interacting with Hi-C files in R Bioconductor version: Release (3.17) R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing…
Supported Tools – MultiQC
Tool Tool Name Description Removes adapter sequences and trims low quality bases from the 3′ end of reads. Overlapping paired-ended reads can be merged into consensus sequences and adapter sequence can be found for paired-ended data if not known. Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data….
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170–S180 (2004). CAS PubMed PubMed Central Google Scholar Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). CAS PubMed Google Scholar Peralta, I. E., Spooner, D. M. & Knapp, S….
Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer
Torre, L. A., Siegel, R. L., Ward, E. M. & Jemal, A. Global cancer incidence and mortality rates and trends—an update. Cancer Epidemiol. Prev. Biomark. 25, 16–27 (2016). Article Google Scholar Gerasimova, E. et al. Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis. Front….