PPT-Ensembl

RNASeq Pipeline Steve Searle Outline of Talk What the Ensembl RNASeq pipeline does Ensembl Pipeline infrastructure How weve modified the process as its scaled up Cloud version. David Wallom . Overview. The problem…. Other communities. The pace of technological change. Using the data. The problem…. New telescopes generate vast amounts of data. Particularly (but not limited to) surveys (SDSS, PAN-STARRS, LOFAR, SKA…). Ensembl. and . InterPro. Yanbin Yin. Fall 2014. 1. http://. www.ebi.ac.uk. /training/online/course. /. Homework 3. Go to . http://www.ebi.ac.uk/interpro/training.html. and finish the second online training course “Introduction to protein classification at the EBI” and then answer the following questions:. The . EnsEMBL. Project. Michael Gray. Bristol & Bath Perl Mongers. DNA makes RNA makes protein. EnsEMBL. REST API. API from . perl. Friday 20 September 2013. http://. www.jeansforgenesday.org. /. Welcome to . PolyMarker. !. http://polymarker.tgac.ac.uk/. How to use Biomart to find SNP markers www.wheat-training.com. Options:. Design your own primers. Download pre-designed primers for SNP data. . dynamics. exon f. exon g. n. o f/g. wt. f/g. w. g. w. f. C. onformations averaged over 2 replicates of 50-ns MD simulations. a. b. c. d. e. f/g. i. I. j. n. p. Human. . isoforms. . conformational. Genomics Lesson . 7_3. Hardison. 3/1/15. 1. 3. approaches . to gene predictions. Evidence-based. Transcribed regions. Align to mRNA sequence from the same species. Align to spliced ESTs from the same species. Marina DiStefano, Ph.D.. Clinical Molecular Genetics Fellow, . Harvard Medical School Genetics Training Program. Biocurator Call, 1.10.19. Outline. Why does transcript curation matter? Examples from Hearing Loss. EGI Technical Forum 2012 . The Clarion Congress Hotel, . Freyova. 945/33, Prague. 18 September 2012. Andrew Lyall PhD, ELIXIR Project Manager. Distributed Computing for Life-Sciences &. . Medical Research in the Genome-Age.. in . Ensembl Plants. Poznań. ,. 27th-28th . June. 2013. trans-National Infrastructure for Plant Genomic Science. Introduction. Barley. Hordeum vulgare. A. n . important . cereal and model for adaption. Diego Mauricio Riaño Pachón. diego.riano@cena.usp.br. CEN5789. Quinta-feira: Teoria 8:00h - 12:00h. . Quinta-feira: Prática 13:30h - 16:30h. Rules of the game. You are supposed to . come. to class . SPH 247. Statistical Analysis of. Laboratory Data. 1. May 12, 2015. SPH 247 Statistical Analysis of Laboratory Data. AnnotationDbi. and RNA-. Seq. > source. ("http://bioconductor.org/. biocLite.R. However, genomes are large and complex and visualizing this information is not easy. You need to imagine that the raw annotation information, by itself, can be contained in a text file, which could include positional information (coordinates relative to the reference genome) and different features (e.g. annotation type – gene, mRNA, intron/exon, variant, UTR, etc.). . BioMart. to extract SNP information. http://plants.ensembl.org/biomart/martview. How to use Biomart to find SNP markers www.wheat-training.com. How to use Biomart to find SNP markers www.wheat-training.com. “A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of a species’ set of genes”. Public databases.