Hello,

I have never used perl before but would like to analyse some data using a publically available perl script called ProxyGeneLD. (http://ki.se/ki/jsp/polopoly.jsp?d=26072&l=en)

The main command line in the software is this:

Usage: >Perl proxyGeneLD (qry) (rs) (P) (d) r2 5' 3' (qry)- file name that includes SNP list, output of genome-wide association study.

(rs) - column number containing rs numbers of SNPs (P) - column number of P-values

(d) - delimiter used in the (qry) file (Possible options are 'space', 'tab' and 'comma'.)

r2 - threshold of r2 that classifies two SNPs are so highly correlated to join proxy cluster (default is 0.8)

5' - 5' promoter region length that is included as the genic region (default is 1000bp)

3' - possible 3'UTR extension from reference transcript (default is 0bp)

As a complete beginner, I would appreciate it if someone could give me some guidance as to how to format the arguments in the command line - should they be inside the brackets as shown? Do they need to be separated by commas or spaces or something else? Should they be inside quotes?

If someone could give me some guidance on what this command line should look like with realistic example arguments I would really appreciate it.

Thanks.

In reply to Beginner using a downloaded script by TattieSoup

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