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 bb66d5498be3014ccab93ef382d6d05536e6e047..f582b33661a4e858ecbfc2600bf4b5492cd35727 100644 (file)
--- a/README.md
+++ b/README.md
@@ -102,17 +102,26 @@ consideration.
 By default, RSEM automates the alignment of reads to reference
 transcripts using the Bowtie alignment program.  To use an alternative
 alignment program, align the input reads against the file
-'reference_name.idx.fa' generated by 'rsem-prepare-reference', and format
-the alignment output in SAM or BAM format.  Then, instead of providing
-reads to 'rsem-calculate-expression', specify the '--sam' or '--bam' option
-and provide the SAM or BAM file as an argument.  When using an
-alternative aligner, you may also want to provide the '--no-bowtie' option
-to 'rsem-prepare-reference' so that the Bowtie indices are not built.
-
-Some aligners' (other than Bowtie) output might need to be converted
-so that RSEM can use. For conversion, please run
+'reference_name.idx.fa' generated by 'rsem-prepare-reference', and
+format the alignment output in SAM or BAM format.  Then, instead of
+providing reads to 'rsem-calculate-expression', specify the '--sam' or
+'--bam' option and provide the SAM or BAM file as an argument.  When
+using an alternative aligner, you may also want to provide the
+'--no-bowtie' option to 'rsem-prepare-reference' so that the Bowtie
+indices are not built.
+
+RSEM requires all alignments of the same read group together. For
+paired-end reads, RSEM also requires the two mates of any alignment be
+adjacent. To check if your SAM/BAM file satisfy the requirements,
+please run
+
+    rsem-sam-validator <input.sam/input.bam>
+
+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
@@ -160,6 +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