Upload SNPs

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The Upload SNPs page allows you to incorporate data on a set of SNPs from a XML file.

If you try to upload a SNP which already exists in the Study (that is, whose ID is already there), it will not be possible unless you have ticked the option Overwrite if SNP code already exists. In this case all new SNP information for this specific SNP will overwrite the extant one.

To make easier for user to generate the XML files, SNPator provides some Excel files in the Public downloads section. These Excel files incorporate a macro that creates XML files from the spreadsheet.

A possible way to proceed (by no means the only one) would be as follows:

1. Download the Excel files from the Public downloads section:

2. Extract the Excel files from the *.zip file into your local disc.

3. Open the file snps.xls (remember that this file contains macros, so you must set your Excel options to allow macros). The file must look like this (depending on you Microsoft Office version):

4. The first two rows of the spreadsheet must be kept untouched (unless you have defined new Descriptors in the Descriptors administration section). All the information you want to upload into SNPator via XML must be entered into the remaining rows. Only the "code" field is mandatory. The rest of fields may or may not be needed depending on the kind of analysis you plan to perform using SNPator.

To make data entering easier, the "chromosome" and "position" fields can be automatically filled-up by SNPator  once every SNP dbSNP IDs has been uploaded. To do so, remember to fill-up now the "dbsnp" field in order to identify the SNP in the dbSNP public database.

If you have defined some Descriptors for this study, you can add their names in the second row, just after the names of the standard fields. It is very important that these names match exactly the name of the descriptor you entered in the Descriptors Administration section.

5. Once you have entered all the data in the spreadsheet, you should execute the macro embedded in it:

Now just give a name to the XML file that is going to be created and press OK:

You now have a XML file ready to upload to SNPator. After the upload of this file you will get a report in the User Results Section.