#const
my $BURNIN = 200;
-my $CHAINLEN = 1000;
+my $NSAMPLES = 1000;
my $SAMPLEGAP = 1;
my $CONFIDENCE = 0.95;
my $NSPC = 50;
&collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
if ($calcCI) {
- $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $CHAINLEN $SAMPLEGAP";
+ $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $NSAMPLES $SAMPLEGAP";
+ $command .= " -p $nThreads";
if ($quiet) { $command .= " -q"; }
print "$command\n";
$status = system($command);