The order of @SQ tags in SAM/BAM files can be arbitrary now

[rsem.git] / README.md

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+++ b/README.md
@@ -22,15 +22,21 @@ Table of Contents
 ## <a name="introduction"></a> Introduction
 
 RSEM is a software package for estimating gene and isoform expression
-levels from RNA-Seq data.  The new RSEM package (rsem-1.x) provides an
-user-friendly interface, supports threads for parallel computation of
-the EM algorithm, single-end and paired-end read data, quality scores,
-variable-length reads and RSPD estimation. It can also generate
-genomic-coordinate BAM files and UCSC wiggle files for
-visualization. In addition, it provides posterior mean and 95%
-credibility interval estimates for expression levels. For
-visualization, it can also generate transcript-coordinate BAM files
-and visualize them and also models learned.
+levels from RNA-Seq data. The RSEM package provides an user-friendly
+interface, supports threads for parallel computation of the EM
+algorithm, single-end and paired-end read data, quality scores,
+variable-length reads and RSPD estimation. In addition, it provides
+posterior mean and 95% credibility interval estimates for expression
+levels. For visualization, It can generate BAM and Wiggle files in
+both transcript-coordinate and genomic-coordinate. Genomic-coordinate
+files can be visualized by both UCSC Genome browser and Broad
+Institute's Integrative Genomics Viewer (IGV). Transcript-coordinate
+files can be visualized by IGV. RSEM also has its own scripts to
+generate transcript read depth plots in pdf format. The unique feature
+of RSEM is, the read depth plots can be stacked, with read depth
+contributed to unique reads shown in black and contributed to
+multi-reads shown in red. In addition, models learned from data can
+also be visualized. Last but not least, RSEM contains a simulator.
 
 ## <a name="compilation"></a> Compilation & Installation
 
@@ -103,8 +109,10 @@ 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
+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. If the alternative aligner does not satisfy the first
+requirement, you can use 'convert-sam-for-rsem' for conversion. Please run
  
    convert-sam-for-rsem --help
 
@@ -152,7 +160,7 @@ wiggle_name: the name the user wants to use for this wiggle plot
 
 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).
+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.
 
 #### c) Generating Transcript Wiggle Plots
 
@@ -258,6 +266,8 @@ map_file: transcript-to-gene-map file's name.
 RSEM uses the [Boost C++](http://www.boost.org) and
 [samtools](http://samtools.sourceforge.net) libraries.
 
+We thank earonesty for contributing patches.
+
 ## <a name="license"></a> License
 
 RSEM is licensed under the [GNU General Public License v3](http://www.gnu.org/licenses/gpl-3.0.html).