nih-gov/www.ncbi.nlm.nih.gov/SNP/rsfile.html

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HTML

<html><!-- #BeginTemplate "/Templates/dbSNP_new.dwt" --><!-- DW6 --><head>
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<title>Upload RS File</title>
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<meta http-equiv="Content-Type"
content="text/html; charset=iso-8859-1">
<META name="keywords" content="single nucleotide polymorphism, SNP,
sequence variation, genome, gene mapping, population structure, dbSNP,
evolution, microsatellite repeat, phenotype, national center for
biotechnology information, ncbi, national library of medicine, nlm, database,
archive, bioinformatics, national institute of health, ncbi">
<META name="description" content="The Single Nucleotide Polymorphism
database (dbSNP) is a public-domain archive for a broad collection of simple
genetic polymorphisms.">
<META name="author" content="snpdev">
<META name="robots" content="index,nofollow,noarchive">
<meta http-equiv="Expires" content="Wed, 28 Jan 2006 01:01:01 GMT">
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galert(['div#alert', 'body > *:nth-child(1)'])
});
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<script language="JavaScript" src="/corehtml/query/query.js"></script>
<script language="JavaScript" src="/projects/SNP/Javascripts/snputils.js"></script>
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<script language="JavaScript" src="Javascripts/cookies.js"></script>
<script language="JavaScript" src="Javascripts/sidebar.js"></script>
<!-- #BeginEditable "JAVASCRIPT" -->
<SCRIPT LANGUAGE=JAVASCRIPT>
//JAVASCRIPTS start here
function validate()
{
//if ( ( isEmail() ) && ( getSubNum() ) &&( isResultFormat() ) ) {
if ( ( isEmail() ) && ( isResultFormat() ) ) {
// alert("\nEverything appear to be correct.");
winsubmit('./sending.html');
return true;
}
else
{
return false;
}
}
// Checks the E-MAIL field.
function isEmail()
{
// Return false if e-mail field is blank.
if (document.contact.email.value == "")
{
alert("\nThe E-MAIL field is blank.\nPlease enter your e-mail address.")
document.contact.email.focus();
return false;
}
// Return false if e-mail field does not contain a '@' and '.' .
if (document.contact.email.value.indexOf ('@',0) == -1 ||
document.contact.email.value.indexOf ('.',0) == -1)
{
alert("The E-MAIL field requires a \"@\" and a \".\"be used.\nPlease re-enter your e-mail address.")
document.contact.email.select();
document.contact.email.focus();
return false;
}
else
{
return true;
}
}
// Check names field.
function isName()
{
// Return false if name fields is blank.
if (document.contact.firstname.value == "")
{
alert("The First Name field is blank.\nPlease enter your first name.")
document.contact.firstname.focus();
return false;
}
if (document.contact.lastname.value == "")
{
alert("The Last Name field is blank.\nPlease enter your last name.")
document.contact.lastname.focus();
return false;
}
return true;
}
// Check subformat selection
function isSubFormat()
{
// Return false if subformat fields is 0.
if (document.contact.subformat.options.value == 0)
{
alert("\nPlease click on the button 'Select Format'\n and select a submission format for querry.")
return false;
}
else
{
return true;
}
}
//Check SS number input
function getSubNum()
{
//var msg = "getSS()";
//alert ("At " + msg);
a = (document.contact.subnum.value);
if (isNum())
{
a.toLowerCase();
var re = /\r/g;
a = a.replace(re, "\n");
ssArray = new Array();
ssArray = a.split("\n");
if (ssArray.length > 30001)
{
alert ("Your submission exceed the 30000 SNP ID limit!\nPlease remove all IDs below your submission number " + ssArray[999] + " and resubmit.");
return false;
}
index = 0;
for (ssnum in ssArray) {
b = ssArray[index];
if (b.length > 0) {
errCheck();
}
index++;
}
a = ssArray.join("\n");
document.contact.subnum.value = a;
return true;
}
return false;
}
function errCheck()
{ var numstr = /rs\d+$/;
while (!(b.match(numstr)) ) {
// alert (b + " is incorrect format!\nNumbers should have the prefix \"rs\" and a number \n (eg. ss23131)");
b = prompt(b + " is not correct!\nThe submission should have the prefix \"rs\" and a number (eg. rs23131)\nPlease enter a new RS number for " + b + ".");
b.toLowerCase();
}
// isNum();
ssArray[index] = b;
return true;
}
function isNum()
{
if (document.contact.subnum.value == "")
{
alert("You did not enter a RS number.")
document.contact.subnum.focus();
return false;
}
else
{
return true;
}
}
// Check subformat selection
function isResultFormat()
{
// Return false if subformat fields is 0.
var selection = document.contact.result_option;
var outformat = selection.options[selection.selectedIndex].value;
//alert( outformat + "\n" );
if (outformat == "" )
{
alert("\nPlease click on the button 'FORMAT'\n and select an output format.")
return false;
}
else
{
return true;
}
}
function winsubmit(ThisUrl)
{
FormatHelp=window.open(ThisUrl,"Format_Help","height=200,width=200,left=200,top=200,scrollbars=no,resizable=no,status=no");
}
function win(ThisUrl)
{
FormatHelp=window.open(ThisUrl,"Format_Help","height=300,width=450,left=20,top=80,scrollbars=yes,resizable=yes,status=yes");
}
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<noscript>See Human Variations Search</noscript><!-- #EndLibraryItem --><SPAN class="GUTTER1"><BR>
</SPAN> </td>
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<td width="5"> <img src="corehtml/spacer10.GIF"
width="3" height="1" border="0" alt="Spacer gif"> </td>
<!-- right content column -->
<!-- #BeginEditable "SNP_right column" -->
<td width="460">
<form name="contact" method="post" enctype="multipart/form-data" onSubmit="return validate()" action="./batch.cgi" >
<!-- title with bullet -->
<table
border="0" width="460" cellspacing="2" cellpadding="0" bgcolor="#FFFFFF">
<tr>
<td width="7" bgcolor="#315399">&nbsp;</td>
<td width="453" bgcolor="#CCCCFF" class="H3"><b><font size="5">Email</font></b></td>
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<br /><!-- #BeginLibraryItem "/Library/Batch_email_input.lbi" --><style type="text/css">
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<table>
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<td> </td>
<td><!-- #BeginLibraryItem "/Library/BatchQueryNotice.lbi" -->
<table width="240" border="0">
<tr>
<td bgcolor="#FFFFCC">
<em><strong>NOTICE: BED file format update and name change</strong></em><br>
<div class="annoucementbox">
<PRE>The dbSNP BED format has been updated to comply with current
standard BED specifications
(https://genome.ucsc.edu/FAQ/FAQformat.html#format1 ); it has been QA tested
and is compatible with standard BED tools and genome browser uploads such as
the NCBI Remap Service (https://www.ncbi.nlm.nih.gov/genome/tools/remap), the
UCSC Genome browser (https://genome.ucsc.edu/cgi-bin/hgGateway) and the EBI
Genome Browser (http://www.ensembl.org).
The BED format update replaces dbSNP's 30 field BED format
(https://ftp.ncbi.nih.gov/snp/specs/BED_rsDocsum_Mapping.README.txt) with a
format that contains only three required fields and three optional fields:
Required Fields:
1. chrom: The name of the chromosome (e.g. chr1, chr2, etc.).
2. chromStart: The Reference SNP (rs) start position on the chromosome.
Note: The first base in a chromosome is numbered 0.
3. chromEnd: The rs end position on the chromosome.
Optional Fields:
4. name: The dbSNP Reference SNP (rs) ID
5. score: dbSNP does not assign a score value, so this field will always
contain a 0 .
6. strand: This field defines strand orientation as either + or -.
The previous 30 field format is now known as the <strong>BED Extended</strong> format in the
output format selection below.
Please send corrections and comments to snp-admin@ncbi.nlm.nih.gov.
Regards,
dbSNP Production Team
</PRE>
</div>
</td>
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<br>
<!--
<p class="style1">Dear Users:</p>
<p class="style1">Batch query service is currently offline for repair. We'll try to restore service by next Monday Feb 11, 2008. Please contact snp-admin@ncbi.nlm.nih.gov if you have any concerns. </p>
<p class="style1">We apologize for the inconvenience and thank you for your patience. </p>
<p class="style1">Regards,</p>
<p class="style1">dbSNP Development Team</p>
<p class="style1">&nbsp;</p>
--><!-- #EndLibraryItem --><p>The limit for each batch request is 30,000 IDs (ss#,rs#, etc.). A batch larger than the limit will be rejected. However, there's no limit to the number of batches submitted. </p>
<p>Requested data will be sent to the email address you provide
below.&nbsp;<br>
(<span class="style1">Please enter only one email address per request</span>) </p></td>
</tr>
<tr>
<td> </td>
<td>
<input tabindex="1" name="email" size=60 value="">
</td>
</tr>
</table>
<table
border="0" width="460" cellspacing="2" cellpadding="0" bgcolor="#FFFFFF">
<tr>
<td width="7" bgcolor="#315399">&nbsp;</td>
<td width="453" bgcolor="#CCCCFF" class="H3"><b><font size="5">Organism</font></b></td>
</tr>
</table>
&nbsp;&nbsp;
<select tabindex="2"name="organism">
<TMPL_LOOP NAME="ORGANISMS">
<TMPL_IF NAME="selected">
<option value='<TMPL_VAR NAME="database_name">' selected><TMPL_VAR NAME="organism"></option>
<TMPL_ELSE>
<option value='<TMPL_VAR NAME="database_name">'><TMPL_VAR NAME="organism"></option>
</TMPL_IF>
</TMPL_LOOP>
</select>
<!-- <TMPL_LOOP NAME="fruit_loop">
<TR>
<TD><TMPL_VAR NAME="name"></TD>
<TD><TMPL_VAR NAME="color"></TD>
<TD><TMPL_VAR NAME="shape"></TD>
</TR>
</TMPL_LOOP> --><!-- #EndLibraryItem --><input type="hidden" name="subformat" value="rsfile">
<div align="center"> </div>
<table
border="0" width="460" cellspacing="2" cellpadding="0" bgcolor="#FFFFFF">
<tr>
<td width="7" bgcolor="#315399">&nbsp;</td>
<td width="453" bgcolor="#CCCCFF" class="H3"><b><font size="5">Select
Result Format</font></b></td>
</tr>
</table>
<table width="96%" border="0" height="35">
<tr>
<td width="32%"><!-- #BeginLibraryItem "/Library/Batch_result_format_menu.lbi" --><select tabindex="2"
name="result_option">
<option value="BED" selected>BED (6-columns)</option>
<option value="VCF">VCF</option>
<option value="BDX">BED Extended (30-columns)</option>
<option value="ASN">ASN.1</option>
<option value="CHR">CHROMOSOME RPT</option>
<option value="FAS">FASTA</option>
<option value="FLT">FLATFILE</option>
<!-- <option value="XMB">XML(Brief)</option>-->
<option value="XMF">XML(Full)</option>
<option value="SSF">SubSNP Details</option>
<option value="RSR">RS Cluster Report</option>
<option value="GEN">Genotype Report</option>
</select>
<input name="Input" type="hidden" value="<TMPL_VAR NAME='query_key'>">
<input name="Input" type="hidden" value="<TMPL_VAR NAME='webenv'>">
<!-- #EndLibraryItem --></td>
<td width="68%"><!-- #BeginLibraryItem "/Library/corehtml_help.gif.lbi" --><a href="https://ftp.ncbi.nih.gov/snp/00readme.txt" target="_blank"><img src="corehtml/help.gif" width="17" height="17" border="0" alt="Help gif"></a><!-- #EndLibraryItem --></td>
</tr>
</table>
<table
border="0" width="460" cellspacing="2" cellpadding="0" bgcolor="#FFFFFF">
<tr>
<td width="7" bgcolor="#315399">&nbsp;</td>
<td width="453" bgcolor="#CCCCFF" class="H3"><b><font size="5">Upload
a File with rs numbers</font></b></td>
</tr>
</table>
<table>
<tr>
<td>
<input type="file" name="filename" value = "" size=41 />
<br />
</td>
<td>
<input type="submit" value="Submit" name="Submit">
</td>
</tr>
</table>
</form>
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