Hello, Manisha. The problem you are experiencing is due to the fact that these files are extremely large. The file sizes are snp131.txt: 2.82GB, snp132.txt: 6.11GB, snp135.txt: 8.54GB. I have verified that snp135.txt does in fact open properly. Your program can apparently open a file smaller than 3GB, but is having problems opening the larger files. The filenames are based on the build number, so snp135 contains dnSNP build 135. Obviously, build 135 contains the most up-to-date information.
I recommend using our Table Browser to obtain the information you're interested in. If you don't need the entire table, you can select only the information you need. If you do need the entire table, this will enable you to break it into smaller, more manageable pieces. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. The below example will show you how to obtain data from the All SNPs(135) track: 1. Go to http://genome.ucsc.edu 2. On the blue navigation bar at the top of the screen, click "Tables" 3. Set the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Variation and Repeats Track: All SNPs(135) Table: snp135 4. On the "region" line, you can specify a genomic position like "chr21" for all of chromosome 21 or "chr21:33031597-33041570" for only a specific portion of chromosome 21. You can also click the "define regions" button to specify multiple regions. 5. On the "output format" line, set one of the following: "All fields from selected table": Gives you every column of data from the table in your output "Selected fields from primary and related tables": Allows you to specify which columns of data you want in your output (after you click the "get output" button) 6. Click the "get output" button Please note that the Table Browser will likely time out if the data set is too large. If you have access to MySQL, you can also directly query our database. For instructions on how to do so, please see http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29. If for some reason you need snp135.txt in its entirety, I would recommend contacting the software manufacturer (http://454.com/products/analysis-software/index.asp) and asking them about opening files larger than 8GB. 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 Manisha Sent: Sunday, May 13, 2012 10:10 PM To: [email protected]; [email protected] Subject: Re: [Genome] SNP135.txt Dear Sir, I have downloaded human snp135.txt, snp132.txt and snp131.txt files from following link http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ . I have been trying to access Human snp135.txt file for gs Reference Mapper but its showing the file error. Even the same problem persist with snp132.txt but snp 131.txt works properly. Kindly let me know is any file error so that I may decide which one to use. Also let me know what is the difference in the three files. Thanking you Regards Manisha Sajnani Senior Research Fellow Department of Animal Biotechnology Anand Agricultural University Anand _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
