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

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 836a3677770e79db7b571e4fb2542d648986a165..f582b33661a4e858ecbfc2600bf4b5492cd35727 100644 (file)
--- a/README.md
+++ b/README.md
@@ -121,7 +121,7 @@ If your file does not satisfy the requirements, you can use
 'convert-sam-for-rsem' to convert it into a BAM file which RSEM can
 process. Please run
  
-   convert-sam-for-rsem --help
+    convert-sam-for-rsem --help
 
 to get usage information or visit the [convert-sam-for-rsem
 documentation
@@ -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