X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=README.md;h=77c0693af045ab7daa551055dff244905bca111f;hp=b46826a58209fda36bc59cff8e860a95707dfe25;hb=237bbdf363c9e42ee24e2fd63106dccf20d9bf2f;hpb=4a435fbee229af1dd5f76b4feb0ca71398ac8796
diff --git a/README.md b/README.md
index b46826a..77c0693 100644
--- a/README.md
+++ b/README.md
@@ -22,15 +22,21 @@ Table of Contents
## 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.
## 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
@@ -132,24 +140,27 @@ 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). 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
@@ -255,6 +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.
+
## License
RSEM is licensed under the [GNU General Public License v3](http://www.gnu.org/licenses/gpl-3.0.html).