my $sampling = 0;
my $calcPME = 0;
my $calcCI = 0;
-my $var_opt = 0; # temporarily, only for internal use
my $quiet = 0;
my $help = 0;
"output-genome-bam" => \$genGenomeBamF,
"sampling-for-bam" => \$sampling,
"calc-pme" => \$calcPME,
- "var" => \$var_opt,
"calc-ci" => \$calcCI,
"ci-memory=i" => \$NMB,
"samtools-sort-mem=s" => \$SortMem,
if ($sampling) { $command .= " --sampling"; }
if ($seed ne "NULL") { $command .= " --seed $seeds[0]"; }
}
-if ($calcPME || $var_opt || $calcCI) { $command .= " --gibbs-out"; }
+if ($calcPME || $calcCI) { $command .= " --gibbs-out"; }
if ($quiet) { $command .= " -q"; }
&runCommand($command);
if ($mTime) { $time_start = time(); }
-if ($calcPME || $var_opt || $calcCI ) {
+if ($calcPME || $calcCI ) {
$command = "rsem-run-gibbs $refName $imdName $statName $BURNIN $NCV $SAMPLEGAP";
$command .= " -p $nThreads";
- if ($var_opt) { $command .= " --var"; }
if ($seed ne "NULL") { $command .= " --seed $seeds[1]"; }
if ($quiet) { $command .= " -q"; }
&runCommand($command);
contains column names separated by the tab character. The format of
each line in the rest of this file is:
-transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct [pme_expected_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
+transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct [posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
Fields are separated by the tab character. Fields within "[]" are
optional. They will not be presented if neither '--calc-pme' nor
gene has only one isoform or the gene information is not provided,
this field will be set to 100.
-'pme_expected_count', 'pme_TPM', 'pme_FPKM' are posterior mean
-estimates calculated by RSEM's Gibbs sampler. 'IsoPct_from_pme_TPM' is
-the isoform percentage calculated from 'pme_TPM' values.
+'posterior_mean_count', 'pme_TPM', 'pme_FPKM' are posterior mean
+estimates calculated by RSEM's Gibbs
+sampler. 'posterior_standard_deviation_of_count' is the posterior
+standard deviation of counts. 'IsoPct_from_pme_TPM' is the isoform
+percentage calculated from 'pme_TPM' values.
'TPM_ci_lower_bound', 'TPM_ci_upper_bound', 'FPKM_ci_lower_bound' and
'FPKM_ci_upper_bound' are lower(l) and upper(u) bounds of 95%
contains column names separated by the tab character. The format of
each line in the rest of this file is:
-gene_id transcript_id(s) length effective_length expected_count TPM FPKM [pme_expected_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
+gene_id transcript_id(s) length effective_length expected_count TPM FPKM [posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
Fields are separated by the tab character. Fields within "[]" are
optional. They will not be presented if neither '--calc-pme' nor
contains column names separated by the tab character. The format of
each line in the rest of this file is:
-allele_id transcript_id gene_id length effective_length expected_count TPM FPKM AlleleIsoPct AlleleGenePct [pme_expected_count pme_TPM pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
+allele_id transcript_id gene_id length effective_length expected_count TPM FPKM AlleleIsoPct AlleleGenePct [posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
Fields are separated by the tab character. Fields within "[]" are
optional. They will not be presented if neither '--calc-pme' nor