add --no-bam-output option to not generate output bam files

[rsem.git] / README.md

diff --git a/README.md b/README.md
index a4c5ce504a0f284bb594e9a57807a17969a4fc51..bb66d5498be3014ccab93ef382d6d05536e6e047 100644 (file)
--- a/README.md
+++ 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
 ## <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
 
 
 ## <a name="compilation"></a> Compilation & Installation
 


@@ -84,8 +90,8 @@ documentation page](http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-express
 #### Calculating expression values from single-end data
 
 For single-end models, users have the option of providing a fragment
 #### Calculating expression values from single-end data
 
 For single-end models, users have the option of providing a fragment

-length distribution via the --fragment-length-mean and
---fragment-length-sd options.  The specification of an accurate fragment
+length distribution via the '--fragment-length-mean' and
+'--fragment-length-sd' options.  The specification of an accurate fragment

 length distribution is important for the accuracy of expression level
 estimates from single-end data.  If the fragment length mean and sd are
 not provided, RSEM will not take a fragment length distribution into
 length distribution is important for the accuracy of expression level
 estimates from single-end data.  If the fragment length mean and sd are
 not provided, RSEM will not take a fragment length distribution into


@@ -96,12 +102,21 @@ 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
 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
+'reference_name.idx.fa' generated by 'rsem-prepare-reference', and format

 the alignment output in SAM or BAM format.  Then, instead of providing
 the alignment output in SAM or BAM format.  Then, instead of providing

-reads to rsem-calculate-expression, specify the --sam or --bam option
+reads to 'rsem-calculate-expression', specify the '--sam' or '--bam' option

 and provide the SAM or BAM file as an argument.  When using an
 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.
+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
+ 
+   convert-sam-for-rsem --help
+
+to get usage information or visit the [convert-sam-for-rsem
+documentation
+page](http://deweylab.biostat.wisc.edu/rsem/convert-sam-for-rsem.html).

 
 However, please note that RSEM does ** not ** support gapped
 alignments. So make sure that your aligner does not produce alignments
 
 However, please note that RSEM does ** not ** support gapped
 alignments. So make sure that your aligner does not produce alignments


@@ -123,24 +138,27 @@ unsorted BAM file, 'sample_name.genome.sorted.bam' and
 generated by the samtools included. All these files are in genomic
 coordinates.
 
 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
 
 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:    
 
 
 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  
 
 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). 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
 
 
 #### c) Generating Transcript Wiggle Plots
 


@@ -246,6 +264,8 @@ 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.
 
 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).
 ## <a name="license"></a> License
 
 RSEM is licensed under the [GNU General Public License v3](http://www.gnu.org/licenses/gpl-3.0.html).