Added some instructions on how to visualize transcript coordinate BAM/WIG files using IGV

diff --git a/README.md b/README.md
index 6e8acd8fb2df0f100fc6a0622bde5467aa8b649a..f582b33661a4e858ecbfc2600bf4b5492cd35727 100644 (file)
--- a/README.md
+++ b/README.md
@@ -169,6 +169,18 @@ For UCSC genome browser, please refer to the [UCSC custom track help page](http:
 
 For integrative genomics viewer, please refer to the [IGV home page](http://www.broadinstitute.org/software/igv/home). Note: Although IGV can generate read depth plot from the BAM file given, it cannot recognize "ZW" tag RSEM puts. Therefore IGV counts each alignment as weight 1 instead of the expected weight for the plot it generates. So we recommend to use the wiggle file generated by RSEM for read depth visualization.
 
+Here are some guidance for visualizing transcript coordinate files:
+
+1) Import the transcript sequences as a genome 
+
+Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.transcripts.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'.
+
+2) Load visualization files
+
+Select File -> Load from File, then choose one transcript coordinate visualization file generated by RSEM. IGV might require you to convert wiggle file to tdf file. You should use igvtools to perform this task. One way to perform the conversion is to use the following command
+
+    igvtools tile reference_name.transcript.wig reference_name.transcript.tdf reference_name.genome   
+ 
 #### c) Generating Transcript Wiggle Plots
 
 To generate transcript wiggle plots, you should run the

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index c01c70ab2e7067f2a4b2f3683215fd87314645e1..2a09c1570ce7cd45a560b7587568ff106766fd75 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -49,6 +49,7 @@ my $genBamF = 1;  # default is generating transcript bam file
 my $genGenomeBamF = 0;
 my $sampling = 0;
 my $calcCI = 0;
+my $var_opt = 0; # temporarily, only for internal use
 my $quiet = 0;
 my $help = 0;
 
@@ -89,6 +90,7 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
           "no-bam-output" => sub { $genBamF = 0; },
           "output-genome-bam" => \$genGenomeBamF,
           "sampling-for-bam" => \$sampling,
+          "var" => \$var_opt,
           "calc-ci" => \$calcCI,
           "ci-memory=i" => \$NMB,
           "time" => \$mTime,
@@ -291,12 +293,15 @@ if ($mTime) { $time_end = time(); $time_rsem = $time_end - $time_start; }
 
 if ($mTime) { $time_start = time(); }
 
-if ($calcCI) {
+if ($calcCI || $var_opt) {
     $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $NCV $SAMPLEGAP";
     $command .= " -p $nThreads";
+    if ($var_opt) { $command .= " --var"; }
     if ($quiet) { $command .= " -q"; }
     &runCommand($command);
+}
 
+if ($calcCI) {
     system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak1");
     system("mv $sampleName.genes.results $imdName.genes.results.bak1");
     &collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level