my $mTime = 0;
my ($time_start, $time_end, $time_alignment, $time_rsem, $time_ci) = (0, 0, 0, 0, 0);
+my $mate1_list = "";
+my $mate2_list = "";
+my $inpF = "";
+
+my ($refName, $sampleName, $sampleToken, $temp_dir, $stat_dir, $imdName, $statName) = ();
+my $gap = 32;
+
GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
+ "temporary-folder=s" => \$temp_dir,
"no-qualities" => \$no_qual,
"paired-end" => \$paired_end,
"strand-specific" => \$strand_specific,
if ($strand_specific) { $probF = 1.0; }
-my $mate1_list = "";
-my $mate2_list = "";
-my $inpF = "";
-
-my ($refName, $sampleName, $sampleToken, $temp_dir, $stat_dir, $imdName) = ();
-my $gap = 32;
-
if ($paired_end) {
if ($no_qual) { $read_type = 2; }
else { $read_type = 3; }
if ($pos < 0) { $sampleToken = $sampleName; }
else { $sampleToken = substr($sampleName, $pos + 1); }
-$temp_dir = "$sampleName.temp";
+if ($temp_dir eq "") { $temp_dir = "$sampleName.temp"; }
$stat_dir = "$sampleName.stat";
if (!(-d $temp_dir) && !mkdir($temp_dir)) { print "Fail to create folder $temp_dir.\n"; exit(-1); }
if (!(-d $stat_dir) && !mkdir($stat_dir)) { print "Fail to create folder $stat_dir.\n"; exit(-1); }
$imdName = "$temp_dir/$sampleToken";
+$statName = "$stat_dir/$sampleToken";
if (!$is_sam && !$is_bam && !$no_qual && ($phred33 + $phred64 + $solexa == 0)) { $phred33 = 1; }
$command .= " -1 $mate1_list -2 $mate2_list";
}
- $command .= " | gzip > $sampleName.sam.gz";
+ # pipe to samtools to generate a BAM file
+ $command .= " | $dir\sam/samtools view -S -b -o $imdName.bam -";
if ($mTime) { $time_start = time(); }
if ($mTime) { $time_end = time(); $time_alignment = $time_end - $time_start; }
- $inpF = "$sampleName.sam.gz";
- $is_sam = 1; # output of bowtie is a sam file
+ $inpF = "$imdName.bam";
+ $is_bam = 1; # alignments are outputed as a BAM file
}
if ($mTime) { $time_start = time(); }
-$command = $dir."rsem-parse-alignments $refName $sampleName $sampleToken";
+$command = $dir."rsem-parse-alignments $refName $imdName $statName";
my $samInpType;
if ($is_sam) { $samInpType = "s"; }
print OUTPUT "$L\n";
close(OUTPUT);
-$command = $dir."rsem-run-em $refName $read_type $sampleName $sampleToken -p $nThreads";
+$command = $dir."rsem-run-em $refName $read_type $sampleName $imdName $statName -p $nThreads";
if ($genBamF) {
$command .= " -b $samInpType $inpF";
if ($fn_list ne "") { $command .= " 1 $fn_list"; }
else { $command .= " 0"; }
if ($sampling) { $command .= " --sampling"; }
}
-if ($calcCI) { $command .= " --gibbs-out"; }
+if ($calcCI || $var_opt) { $command .= " --gibbs-out"; }
if ($quiet) { $command .= " -q"; }
&runCommand($command);
+&collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
+&collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
+
if ($genBamF) {
$command = $dir."sam/samtools sort $sampleName.transcript.bam $sampleName.transcript.sorted";
&runCommand($command);
}
}
-&collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
-&collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
-
if ($mTime) { $time_end = time(); $time_rsem = $time_end - $time_start; }
if ($mTime) { $time_start = time(); }
if ($calcCI || $var_opt) {
- $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $NCV $SAMPLEGAP";
+ $command = $dir."rsem-run-gibbs $refName $imdName $statName $BURNIN $NCV $SAMPLEGAP";
$command .= " -p $nThreads";
if ($var_opt) { $command .= " --var"; }
if ($quiet) { $command .= " -q"; }
&collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
&collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
- $command = $dir."rsem-calculate-credibility-intervals $refName $sampleName $sampleToken $CONFIDENCE $NCV $NSPC $NMB";
+ $command = $dir."rsem-calculate-credibility-intervals $refName $imdName $statName $CONFIDENCE $NCV $NSPC $NMB";
$command .= " -p $nThreads";
if ($quiet) { $command .= " -q"; }
&runCommand($command);
=item B<--sampling-for-bam>
-When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled and outputed according to the posterior probabilities. If the sampling result is that the read comes from the "noise" transcript, nothing is outputed. (Default: off)
+When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
=item B<--calc-ci>
Keep temporary files generated by RSEM. RSEM creates a temporary directory, 'sample_name.temp', into which it puts all intermediate output files. If this directory already exists, RSEM overwrites all files generated by previous RSEM runs inside of it. By default, after RSEM finishes, the temporary directory is deleted. Set this option to prevent the deletion of this directory and the intermediate files inside of it. (Default: off)
+=item B<--temporary-folder> <string>
+
+Set where to put the temporary files generated by RSEM. If the folder specified does not exist, RSEM will try to create it. (Default: sample_name.temp)
+
=item B<--time>
Output time consumed by each step of RSEM to 'sample_name.time'. (Default: off)
posterior probability of that alignment being the true mapping of a
read. In addition, RSEM pads a new tag ZW:f:value, where value is a
single precision floating number representing the posterior
-probability.
+probability. Because this file contains all alignment lines produced
+by bowtie or user-specified aligners, it can also be used as a
+replacement of the aligner generated BAM/SAM file. For paired-end
+reads, if one mate has alignments but the other does not, this file
+marks the alignable mate as "unmappable" (flag bit 0x4) and appends an
+optional field "Z0:A:!".
'sample_name.transcript.sorted.bam' and
'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
'sample_name.genome.sorted.bam' and 'sample_name.genome.sorted.bam.bai' are the
sorted BAM file and indices generated by samtools (included in RSEM package).
-=item B<sample_name.sam.gz>
-
-Only generated when the input files are raw reads instead of SAM/BAM format files
-
-It is the gzipped SAM output produced by bowtie aligner.
-
=item B<sample_name.time>
Only generated when --time is specified.
projects / rsem.git / blobdiff