Try:

$ mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e "select name,name2 from refGene" > Refseq2Gene.txt

This will give u the mapping file. For mouse replace hg19 with mm10.

You could try bioDBnet converter: http://biodbnet.abcc.ncifcrf.gov/db/db2db.php

You can use Biomart http://crazyhottommy.blogspot.com/2014/09/converting-gene-ids-using-bioconductor.html

An alternate way would be to go to

1) http://genome.ucsc.edu/cgi-bin/hgTables?command=start

2) Select your genome and assembly and selct Genes and Gene Prediction track as group.

3) Select Refseq Genes as track

4) Select refGene as a table and then output the file.

Then you can use a script or excel to map your refseqids to gene names. Make sure you follow what Steve mentioned in the comment section. Also, have u ever used DAVID (http://david.abcc.ncifcrf.gov/conversion.jsp)

Here is a bioperl script

#!/bin/perl
use warnings;
use strict;
use Bio::Perl;
$| = 1;

my $db = new Bio::DB::RefSeq;

print "Input RefSeq ID: ";
my $refseq = <STDIN>;
chomp($refseq);

my $seq = get_sequence('refseq',$refseq);

# most of the time RefSeq_ID eq RefSeq acc
#my $seq = $db->get_Seq_by_id($refseq); # RefSeq ID
#print "accession is ", $seq->accession_number, "\n";

if ($seq->desc =~ /\((\w+)\)/) {
    print"found: $1\n";
    print $seq->desc;
}
else
{
    print "defintion is ", $seq->desc, "\n";
}

Cistrome/Galaxy can do it very easily. http://cistrome.org/ap/ In the tool box on the left:

Liftover/Others Convert between RefSeq, Gene Symbols to Entrez IDs using Bioconductor. Liftover Wig Files Liftover wig files [Galaxy]Convert genome coordinates between assemblies and genomes Standardize wig file Standardize a wig file to a given span Extract data from Wiggle Extract data for certain chromosome from a wiggle file Extract data from Bed Extract data for certain chromosome from a BED file