4 [Bo Li](http://pages.cs.wisc.edu/~bli) \(bli at cs dot wisc dot edu\)
11 * [Introduction](#introduction)
12 * [Compilation & Installation](#compilation)
15 * [Simulation](#simulation)
16 * [Acknowledgements](#acknowledgements)
21 <h2 id="introduction">Introduction</h2>
23 RSEM is a software package for estimating gene and isoform expression
24 levels from RNA-Seq data. The new RSEM package (rsem-1.x) provides an
25 user-friendly interface, supports threads for parallel computation of
26 the EM algorithm, single-end and paired-end read data, quality scores,
27 variable-length reads and RSPD estimation. It can also generate
28 genomic-coordinate BAM files and UCSC wiggle files for visualization. In
29 addition, it provides posterior mean and 95% credibility interval
30 estimates for expression levels.
32 <h2 id="compilation">Compilation & Installation</h2>
34 To compile RSEM, simply run
38 To install, simply put the rsem directory in your environment's PATH
43 To take advantage of RSEM's built-in support for the Bowtie alignment
44 program, you must have [Bowtie](http://bowtie-bio.sourceforge.net) installed.
46 <h2 id="usage">Usage</h2>
48 ### I. Preparing Reference Sequences
50 RSEM can extract reference transcripts from a genome if you provide it
51 with gene annotations in a GTF file. Alternatively, you can provide
52 RSEM with transcript sequences directly.
54 Please note that GTF files generated from the UCSC Table Browser do not
55 contain isoform-gene relationship information. However, if you use the
56 UCSC Genes annotation track, this information can be recovered by
57 downloading the knownIsoforms.txt file for the appropriate genome.
59 To prepare the reference sequences, you should run the
60 'rsem-prepare-reference' program. Run
62 rsem-prepare-reference --help
64 to get usage information or visit the [rsem-prepare-reference
65 documentation page](rsem-prepare-reference.html).
67 ### II. Calculating Expression Values
69 To calculate expression values, you should run the
70 'rsem-calculate-expression' program. Run
72 rsem-calculate-expression --help
74 to get usage information or visit the [rsem-calculate-expression
75 documentation page](rsem-calculate-expression.html).
77 #### Calculating expression values from single-end data
79 For single-end models, users have the option of providing a fragment
80 length distribution via the --fragment-length-mean and
81 --fragment-length-sd options. The specification of an accurate fragment
82 length distribution is important for the accuracy of expression level
83 estimates from single-end data. If the fragment length mean and sd are
84 not provided, RSEM will not take a fragment length distribution into
87 #### Using an alternative aligner
89 By default, RSEM automates the alignment of reads to reference
90 transcripts using the Bowtie alignment program. To use an alternative
91 alignment program, align the input reads against the file
92 'reference_name.idx.fa' generated by rsem-prepare-reference, and format
93 the alignment output in SAM or BAM format. Then, instead of providing
94 reads to rsem-calculate-expression, specify the --sam or --bam option
95 and provide the SAM or BAM file as an argument. When using an
96 alternative aligner, you may also want to provide the --no-bowtie option
97 to rsem-prepare-reference so that the Bowtie indices are not built.
99 ### III. Visualization
101 RSEM contains a version of samtools in the 'sam' subdirectory. When
102 users specify the --out-bam option RSEM will produce three files:
103 'sample_name.bam', the unsorted BAM file, 'sample_name.sorted.bam' and
104 'sample_name.sorted.bam.bai' the sorted BAM file and indices generated
105 by the samtools included.
107 #### a) Generating a UCSC Wiggle file
109 A wiggle plot representing the expected number of reads overlapping
110 each position in the genome can be generated from the sorted BAM file
111 output. To generate the wiggle plot, run the 'rsem-bam2wig' program on
112 the 'sample_name.sorted.bam' file.
116 rsem-bam2wig bam_input wig_output wiggle_name
118 bam_input: sorted bam file
119 wig_output: output file name, e.g. output.wig
120 wiggle_name: the name the user wants to use for this wiggle plot
122 #### b) Loading a BAM and/or Wiggle file into the UCSC Genome Browser
124 Refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/help/customTrack.html).
126 <h2 id="example">Example</h2>
128 Suppose we download the mouse genome from UCSC Genome Browser. We will
129 use a reference_name of 'mm9'. We have a FASTQ-formatted file,
130 'mmliver.fq', containing single-end reads from one sample, which we call
131 'mmliver_single_quals'. We want to estimate expression values by using
132 the single-end model with a fragment length distribution. We know that
133 the fragment length distribution is approximated by a normal
134 distribution with a mean of 150 and a standard deviation of 35. We wish
135 to generate 95% credibility intervals in addition to maximum likelihood
136 estimates. RSEM will be allowed 1G of memory for the credibility
137 interval calculation. We will visualize the probabilistic read mappings
140 The commands for this scenario are as follows:
142 rsem-prepare-reference --gtf mm9.gtf --mapping knownIsoforms.txt --bowtie-path /sw/bowtie /data/mm9 /ref/mm9
143 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
144 rsem-bam2wig mmliver_single_quals.sorted.bam mmliver_single_quals.sorted.wig mmliver_single_quals
146 <h2 id="simulation">Simulation</h2>
150 rsem-simulate-reads reference_name estimated_model_file estimated_isoform_results theta0 N output_name [-q]
152 estimated_model_file: File containing model parameters. Generated by
153 rsem-calculate-expression.
154 estimated_isoform_results: File containing isoform expression levels.
155 Generated by rsem-calculate-expression.
156 theta0: fraction of reads that are "noise" (not derived from a transcript).
157 N: number of reads to simulate.
158 output_name: prefix for all output files.
159 [-q] : set it will stop outputting intermediate information.
163 output_name.fa if single-end without quality score;
164 output_name.fq if single-end with quality score;
165 output_name_1.fa & output_name_2.fa if paired-end without quality
167 output_name_1.fq & output_name_2.fq if paired-end with quality score.
169 output_name.sim.isoforms.results, output_name.sim.genes.results : Results estimated based on sample values.
171 <h2 id="acknowledgements">Acknowledgements</h2>
173 RSEM uses randomc.h and mersenne.cpp from
174 <http://lxnt.info/rng/randomc.htm> for random number generation. RSEM
175 also uses the [Boost C++](http://www.boost.org) and
176 [samtools](http://samtools.sourceforge.net) libraries.
178 <h2 id="license">License</h2>
180 RSEM is licensed under the [GNU General Public License v3](http://www.gnu.org/licenses/gpl-3.0.html).