Hello, Negar. Welcome to the world of bioinformatics! As a new user to the Browser, my first suggestion would be to read through some of the help docs: http://genome.ucsc.edu/training.html. I would definitely recommend the OpenHelix tutorial, the Genome Browser User's Guide and the Table Browser User's Guide. You can also find our FAQ section at http://genome.ucsc.edu/FAQ/ and you can search for previously-answered mailing list questions at http://genome.ucsc.edu/contacts.html. When in doubt, you can almost always find the answers to your questions from one of these resources.
There is no simple way to do what you've asked, but it is certainly possible. If you have a list of sequences, the first thing to do would be to obtain genomic coordinates which you can do using our BLAT utility. There is a web-based tool at http://genome.ucsc.edu/cgi-bin/hgBlat and also a command line utility that you can download from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. To use the web-based BLAT tool, simply select your genome, assembly and other options and then paste your sequences into the text box and click the "submit" button. You will be presented with a list of results that best match your sequences. Note that the web-based utility can only run on 25 sequences at a time. If you need to run it on a larger volume of sequences, you should download the command line utility. Once you have your coordinates, you can search for genes that match your coordinates using the Table Browser. The following example will give you a list of genes in the UCSC Genes track from a list of coordinates that you specify: 1. Go to http://genome.ucsc.edu/cgi-bin/hgTables 2. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownGene Region: Click the "define regions" button to paste or upload your list of coordinates Output format: Selecting "all fields from selected table" will list all fields in your output. Selecting "selected fields from primary and related tables" will allow you to specify which fields you would like to include in your output. 3. Click the "get output" button Note that this will just give you a general list of genes and coordinates. If you would like to further break this down into exons, introns, 5' UTR exons, coding exons or 3' UTR exons, select "BED - browser extensible data" as your output format. If you wanted to get a list of CpG islands associated with your coordinates, you can change "group" and "track" to "Regulation" and "CpG Islands". The Table Browser is a powerful tool and I recommend reading the User's Guide and experimenting to become familiar with its many features. I hope this helps! Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Negar Ghahramani Sent: Wednesday, June 27, 2012 3:38 PM To: [email protected] Subject: [Genome] Assigning genomic features to a list of genomic fragments Hello everyone, I am relatively new to this field. I have a list of genomic fragments in excel that I would like to associate with genomic features obtained from USCS tables. I would like to assign them to whole gene, 5'UTR, exon, intron, 3'UTR, TSS, Refseq intergenic, CpG Islands. Is there a quick and easy way to do this. I need detailed step by step guidelines since I have not done it before. Thank you. Any help is appreciated. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
