Updates
Apr 26, 2012 RSEM v1.1.19 is online now. Allowed > 2^31 hits. Added some instructions on how to visualize transcript coordinate BAM/WIG files using IGV. Included EBSeq for downstream differential expression analysis.
Mar 11, 2012 RSEM v1.1.18-modified is online now. This modified version solved a compilation problem for GCC version 4.5.3 or higher.
Mar 11, 2012 RSEM v1.1.18 is online now. Added some user-friendly error messages. Added program 'rsem-sam-validator', users can use this program to check if RSEM can process their SAM/BAM files. Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM files into acceptable BAM files for RSEM.
Feb 8, 2012 RSEM v1.1.17 is online now. Fixed a bug related to parallezation of credibility intervals calculation. Added --no-bam-output option to rsem-calculate-expression. The order of @SQ tags in SAM/BAM files can be arbitrary now.
Jan 31, 2012 RSEM v1.1.16 is online now. Added --time option to show time consumed by each phase. Moved the alignment file out of the temporary folder. Enabled pthreads for calculating credibility intervals.
Jan 26, 2012 RSEM v1.1.15 is online now. Fixed several bugs causing compilation error. Modified samtools' Makefile for cygwin. For cygwin users, please uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM.
Jan 17, 2012 RSEM v1.1.14 is online now. Several things are updated, including transcript coordinate wiggle plot generation. For details, please see what_is_new included in the package.
Nov 5, 2011 RSEM v1.1.13 is online now. Speed up EM algorithm by only updating model parameters for first 10 iterations. Skip reads with its (or at least one of its mates', for paired-end reads) length < 25bp.
Oct 18, 2011 RSEM v1.1.12 is online now. Add a script for generating transcript-to-gene-map file from Trinity output. Claim the minimum seed length explicitly. Allow empty sequences in the reference fasta file.
Aug 25, 2011 RSEM v1.1.11 is online now. A bug related to expected counts calculation is fixed. Allow spaces for field seqname and attributes gene_id and transcript_id in GTF files. This version changed reference indices format used by RSEM, so please rebuild the references by using 'rsem-prepare-reference'.
Aug 10, 2011 RSEM v1.1.10 is online now. Add some user-friendly error messages.
May 27, 2011 RSEM v1.1.9 is online now. "rsem-plot-model" is modified. A bug related to simulation is fixed.
Apr 18, 2011 RSEM v1.1.8 is online now. Added sanity checks for the user choosed aligner, including if the reference used and alignments produced follow RSEM's requirements. Added a new plot for "rsem-plot-model", a histogram of reads with different number of alignments. A bug in "rsem-plot-model" is fixed.
Apr 12, 2011 RSEM v1.1.7 is online now. A bug under transcript set model (i.e. use transcript set as reference) is fixed. This bug will lead crash under transcript set model if user tries to generate BAM format output.
Apr 7, 2011 RSEM v1.1.6 is online now. One bug in 'rsem-plot-model' is fixed. A bug related to assigning task to multiple cpus is fixed.
Mar 21, 2011 RSEM v1.1.5 is online now. Several bugs are fixed. One critical bug relates to set the correct probability of generating a read from forward strand. If users let RSEM run bowtie and do not set the "--strand-specific" option, the bug would make RSEM throw all alignments aligned to forward strand away (by setting the "--forward-prob" as 0). The other two are related to confidence interval calculation. These bugs exist since RSEM v1.1.0. It is important for users to update to this version.
Mar 10, 2011 RSEM v1.1.4 is online now. Provide script for visulazing the model learned from data.
Mar 9, 2011 RSEM v1.1.3 is online now. Fixed a bug related to output format. Grand read/executation permessions to files.
Feb 17, 2011 RSEM v1.1.2 is online now. There are two important changes. First, Normalized Read Fraction(nrf) are eliminated from outputs and posterior mean counts are added. Second, a bug leading RSEM fail if estimating RSPD is fixed. In addition, now RSEM supports SAM Spec v1.3 as well as the old specs.
Feb 10, 2011 RSEM v1.1.1 is online now. Bugs for single end read model are fixed.
Feb 8, 2011 RSEM v1.1.0 is online now. The interfaces are redesigned, correction scheme added and bugs for generating wiggle plots are fixed. Please re-download if you have downloaded this version before Feb 9, 2011. Help information is changed a bit.
Nov 18, 2010 RSEM v1.0.8 is online now. RSEM can calculate credibility intervals now.
Oct 31, 2010 RSEM v1.0.7 is online now. Fix one bug for 32bit machines and one underflow problem.
Sept 27, 2010 RSEM v1.0.6 is online now. Fix a bug in rsem-simulate-reads.
Sept 24, 2010 RSEM v1.0.5 is online now. This is a brand new version of RSEM! Previous version of rsem is obsoleted. Old page is here.
Author
RSEM is mainly developed by Bo Li, who is a member of Deweylab.License
RSEM is under the GNU General Public License
Source Code
Documentation
Prebuilt RSEM Indices for Galaxy Wrapper
These indices are based on RefSeq containing NM accession numbers only. That means only curated genes (no experimental, no miRNA, no noncoding). Only mature RNAs. In addition, 125bp Poly(A) tails are added at the end of each transcript.
Mouse Indices, extracted from mouse genome mm9
Human Indices, extracted from human genome hg18
Simulation Data
Simulation Data using Refseq set as reference
Simulation Data using Ensembl set as reference
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Acknowledgements
RSEM was developed with the help of Prof. Colin Dewey.
(last modified on Apr 26, 2012)