X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;h=6e8acd8fb2df0f100fc6a0622bde5467aa8b649a;hb=543f20967e693ef9150eddc94e7869ed04bad962;hp=a4c5ce504a0f284bb594e9a57807a17969a4fc51;hpb=227db580833c14aa755c84ccb5401ce8c298e225;p=rsem.git
diff --git a/README.md b/README.md
index a4c5ce5..6e8acd8 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
@@ -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
-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
@@ -96,12 +102,30 @@ 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.
+'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
+
+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
+
+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
@@ -123,24 +147,27 @@ 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
@@ -246,6 +273,8 @@ 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).