Hello, The complete genomic is available from our ftp server.
http://genome.ucsc.edu/FAQ/FAQdownloads#download1 Using a tool like BLAT should be help with alignment if the output has been validated (these types of shorter reads that have poor quality will not align well). Whether to compare against the entire genome or a targeted region is a scientific decision that will be a part of the dataflow your team develops. We do have several tools for extracting portions of genomic out of the mail file and different file formats available. Obtaining our source tree and exploring the utilities is recommended, unless you already have your own tools developed: http://genome.ucsc.edu/FAQ/FAQdownloads#download27 http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities General FAQ: http://genome.ucsc.edu/FAQ To navigate the files before ftp (to understand contents), use the Downloads page: http://hgdownload.cse.ucsc.edu/downloads.html For example: Downloads -> Human -> Feb. 2009 -> "Full data set" or "Data set by chromosome" Hopefully this will get you started, please let us know if you have more questions, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Valeria Vasta" <[email protected]> wrote: > From: "Valeria Vasta" <[email protected]> > To: [email protected] > Sent: Monday, August 17, 2009 9:11:07 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] how to create reference sequence files for Illumina analyzer > > Hello > > > > I have to create the reference file for human genome seq. Do I > download > one chromosome at a time or is there a file that contains all? > > > > could you please let me know how to create a reference file with > captureed targeted regions in order to use it to align the sequence > data > from the Illumina genome analyzer? > > > > I suppose there's a way to do it starting with the target coordinates > and should one add some extra 5'-3'? > > > > thanks > > > > Valeria > > > > CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information protected by law. Any > unauthorized review, use, disclosure or distribution is prohibited. > If you are not the intended recipient, please contact the sender by > reply e-mail and destroy all copies of the original message. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
