+++ /dev/null
-README for RSEM
-===============
-
-[Bo Li](http://pages.cs.wisc.edu/~bli) \(bli at cs dot wisc dot edu\)
-
-* * *
-
-Table of Contents
------------------
-
-* [Introduction](#introduction)
-* [Compilation & Installation](#compilation)
-* [Usage](#usage)
-* [Example](#example)
-* [Simulation](#simulation)
-* [Acknowledgements](#acknowledgements)
-* [License](#license)
-
-* * *
-
-<h2 id="introduction">Introduction</h2>
-
-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.
-
-<h2 id="compilation">Compilation & Installation</h2>
-
-To compile RSEM, simply run
-
- make
-
-To install, simply put the rsem directory in your environment's PATH
-variable.
-
-### Prerequisites
-
-To take advantage of RSEM's built-in support for the Bowtie alignment
-program, you must have [Bowtie](http://bowtie-bio.sourceforge.net) installed.
-
-<h2 id="usage">Usage</h2>
-
-### I. Preparing Reference Sequences
-
-RSEM can extract reference transcripts from a genome if you provide it
-with gene annotations in a GTF file. Alternatively, you can provide
-RSEM with transcript sequences directly.
-
-Please note that GTF files generated from the UCSC Table Browser do not
-contain isoform-gene relationship information. However, if you use the
-UCSC Genes annotation track, this information can be recovered by
-downloading the knownIsoforms.txt file for the appropriate genome.
-
-To prepare the reference sequences, you should run the
-'rsem-prepare-reference' program. Run
-
- rsem-prepare-reference --help
-
-to get usage information or visit the [rsem-prepare-reference
-documentation page](rsem-prepare-reference.html).
-
-### II. Calculating Expression Values
-
-To calculate expression values, you should run the
-'rsem-calculate-expression' program. Run
-
- rsem-calculate-expression --help
-
-to get usage information or visit the [rsem-calculate-expression
-documentation page](rsem-calculate-expression.html).
-
-#### 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 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
-consideration.
-
-#### Using an alternative aligner
-
-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.
-
-### III. Visualization
-
-RSEM contains a version of samtools in the 'sam' subdirectory. When
-users specify the --out-bam option RSEM will produce three files:
-'sample_name.bam', the unsorted BAM file, 'sample_name.sorted.bam' and
-'sample_name.sorted.bam.bai' the sorted BAM file and indices generated
-by the samtools included.
-
-#### a) Generating a UCSC Wiggle file
-
-A wiggle plot representing the expected number of reads overlapping
-each position in the genome can be generated from the sorted BAM file
-output. To generate the wiggle plot, run the 'rsem-bam2wig' program on
-the 'sample_name.sorted.bam' file.
-
-Usage:
-
- rsem-bam2wig bam_input wig_output wiggle_name
-
-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
-
-Refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/help/customTrack.html).
-
-<h2 id="example">Example</h2>
-
-Suppose we download the mouse genome from UCSC Genome Browser. We will
-use a reference_name of 'mm9'. We have a FASTQ-formatted file,
-'mmliver.fq', containing single-end reads from one sample, which we call
-'mmliver_single_quals'. We want to estimate expression values by using
-the single-end model with a fragment length distribution. We know that
-the fragment length distribution is approximated by a normal
-distribution with a mean of 150 and a standard deviation of 35. We wish
-to generate 95% credibility intervals in addition to maximum likelihood
-estimates. RSEM will be allowed 1G of memory for the credibility
-interval calculation. We will visualize the probabilistic read mappings
-generated by RSEM.
-
-The commands for this scenario are as follows:
-
- rsem-prepare-reference --gtf mm9.gtf --mapping knownIsoforms.txt --bowtie-path /sw/bowtie /data/mm9 /ref/mm9
- rsem-calculate-expression --bowtie-path /sw/bowtie --phred64-quals --fragment-length-mean 150.0 --fragment-length-sd 35.0 -p 8 --out-bam --calc-ci --memory-allocate 1024 /data/mmliver.fq /ref/mm9 mmliver_single_quals
- rsem-bam2wig mmliver_single_quals.sorted.bam mmliver_single_quals.sorted.wig mmliver_single_quals
-
-<h2 id="simulation">Simulation</h2>
-
-### Usage:
-
- rsem-simulate-reads reference_name estimated_model_file estimated_isoform_results theta0 N output_name [-q]
-
-estimated_model_file: File containing model parameters. Generated by
-rsem-calculate-expression.
-estimated_isoform_results: File containing isoform expression levels.
-Generated by rsem-calculate-expression.
-theta0: fraction of reads that are "noise" (not derived from a transcript).
-N: number of reads to simulate.
-output_name: prefix for all output files.
-[-q] : set it will stop outputting intermediate information.
-
-### Outputs:
-
-output_name.fa if single-end without quality score;
-output_name.fq if single-end with quality score;
-output_name_1.fa & output_name_2.fa if paired-end without quality
-score;
-output_name_1.fq & output_name_2.fq if paired-end with quality score.
-
-output_name.sim.isoforms.results, output_name.sim.genes.results : Results estimated based on sample values.
-
-<h2 id="acknowledgements">Acknowledgements</h2>
-
-RSEM uses randomc.h and mersenne.cpp from
-<http://lxnt.info/rng/randomc.htm> for random number generation. RSEM
-also uses the [Boost C++](http://www.boost.org) and
-[samtools](http://samtools.sourceforge.net) libraries.
-
-<h2 id="license">License</h2>
-
-RSEM is licensed under the [GNU General Public License v3](http://www.gnu.org/licenses/gpl-3.0.html).
projects / rsem.git / commitdiff