CHGV (Duke University) PLOS Genetics: A Peer-Reviewed Open-Access Journal Data | 1000 Genomes Sample lists and sequencing progress A summary of sequencing done for each of the three pilot projects is available here. The list of samples and allocations is provided in a spreadsheet. Variant Calls Our variant calls are always released in vcf format. The released can be found in the release directory EBI|NCBI. Alignments The main project alignments are available in BAM format. Raw sequence files The main project raw sequence data is available in fastq format. Download data The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via our mirrored ftp sites. EBI FTP: NCBI FTP: Users in the Americas should use the NCBI ftp site and users in Europe and the rest of the world should use the EBI ftp site The data is also available via an Aspera server from both sites. An example command line for ascp looks like: FTP Hierachy The data dir The technical dir
PLINK This page describes some basic file formats, convenience functions and analysis options for rare copy number variant (CNV) data. Support for common copy number polymorphisms (CNPs) is described here. Copy number variants are represented as segments. Basic support for segmental CNV data The basic command for reading a list of segmental CN variants is plink --cnv-list mydata.cnv --fam mydata.fam --map mydata.cnv.map which can be abbreviated plink --cfile mydata (note that the map file must have the .cnv.map map extension). FID Family ID IID Individual ID CHR Chromosome BP1 Start position (base-pair) BP2 End position (base-pair) TYPE Type of variant, e.g. 0,1 or 3,4 copies SCORE Confidence score associated with variant SITES Number of probes in the variant Having a header row is optional; if the first line starts with FID it will be ignored. The FAM file format is the first 6 fields of a PED file, described here; this file lists the sex, phenotype and founder status of each individual. and then
All About The Human Genome Project (HGP) All About The Human Genome Project (HGP) The Human Genome Project (HGP) was one of the great feats of exploration in history - an inward voyage of discovery rather than an outward exploration of the planet or the cosmos; an international research effort to sequence and map all of the genes - together known as the genome - of members of our species, Homo sapiens. Completed in April 2003, the HGP gave us the ability, for the first time, to read nature's complete genetic blueprint for building a human being. In this section, you will find access to a wealth of information on the history of the HGP, its progress, cast of characters and future. Educational Resources An Interactive Timeline of the Human Genome [unlockinglifescode.org] An interactive, hyper-linked timeline of genetics that takes the reader from Mendel (1865) to the completion of the mapping of the human genome (2003). Top of page General Information Research Model Organisms To view the PDFs on this page you will need Adobe Reader.
User Page - sbgn.org SBGN study guide Visit the Documents section for: various examples (to get a better idea of what an actual map looks like) some tutorials (very accessible, but not always up-to-date) publications about SBGN (a good start for a brief historical overview) detailed technical specifications (the ultimate reference documents, most up-to-date, but a steep learning curve for beginners) some Frequently Asked Questions Please also check the SBGN PD User Manual when you are ready to draw your own maps. Quick overview The Systems Biology Graphical Notation comprises three complementary languages suited to represent different types of pathways. Process Descriptions (PD) is a language that permits the description of the processes (e.g. biochemical reactions) taking place in a biological system. Entity Relationships (ER) is a language that permits the description of all the relations involving the entities of a biological system. Language reference cards SBGN Bricks dictionary Getting started User Manual
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