relax the requirement about GTF attribute format

[rsem.git] / README.md

diff --git a/README.md b/README.md
index b46826a58209fda36bc59cff8e860a95707dfe25..6076ce665d58704f638be04675ce20c2e57c959d 100644 (file)
--- a/README.md
+++ b/README.md
@@ -132,24 +132,27 @@ unsorted BAM file, 'sample_name.genome.sorted.bam' and
 generated by the samtools included. All these files are in genomic
 coordinates.
 
-#### a) Generating a UCSC Wiggle file
+#### a) Generating a Wiggle file
 
 A wiggle plot representing the expected number of reads overlapping
-each position in the genome can be generated from the sorted genome
-BAM file output.  To generate the wiggle plot, run the 'rsem-bam2wig'
-program on the 'sample_name.genome.sorted.bam' file.
+each position in the genome/transcript set can be generated from the
+sorted genome/transcript BAM file output.  To generate the wiggle
+plot, run the 'rsem-bam2wig' program on the
+'sample_name.genome.sorted.bam'/'sample_name.transcript.sorted.bam' file.
 
 Usage:    
 
-    rsem-bam2wig bam_input wig_output wiggle_name
+    rsem-bam2wig sorted_bam_input wig_output wiggle_name
 
-bam_input: sorted bam file   
+sorted_bam_input: sorted bam file   
 wig_output: output file name, e.g. output.wig   
 wiggle_name: the name the user wants to use for this wiggle plot  
 
-#### b) Loading a BAM and/or Wiggle file into the UCSC Genome Browser
+#### b) Loading a BAM and/or Wiggle file into the UCSC Genome Browser or Integrative Genomics Viewer(IGV)
 
-Refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/help/customTrack.html).
+For UCSC genome browser, please refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/help/customTrack.html).
+
+For integrative genomics viewer, please refer to the [IGV home page](http://www.broadinstitute.org/software/igv/home).
 
 #### c) Generating Transcript Wiggle Plots