Nov 22, 2013   RSEM v1.2.8 is online now. Provided a more detailed description for how to simulate RNA-Seq data using 'rsem-simulate-reads'. Provided more user-friendly error message if RSEM fails to extract transcript sequences due to the failure of reading certain chromosome sequences.
Sept 25, 2013   RSEM v1.2.7 has a minor update. One line is added to the 'WHAT_IS_NEW' file to reflect a change made but forgotten to put in to 'WHAT_IS_NEW'. The line added is "Renamed '--phred33-quals', '--phred64-quals', and '--solexa-quals' in 'rsem-calculate-expression' to '--bowtie-phred33-quals', '--bowtie-phred64-quals', and '--bowtie-solex-quals' to avoid confusion".
Sept 7, 2013   RSEM v1.2.7 is online now. 'rsem-find-DE' is replaced by 'rsem-run-ebseq' and 'rsem-control-fdr' for a more friendly user experience. Added support for differential expression testing on more than 2 conditions in RSEM's EBSeq wrappers 'rsem-run-ebseq' and 'rsem-control-fdr'.
Jul 31, 2013   RSEM v1.2.6 is online now. Install the latest version of EBSeq from Bioconductor and if fails, try to install EBSeq v1.1.5 locally. Fixed a bug in 'rsem-gen-transcript-plots', which makes 'rsem-plot-transcript-wiggles' fail.
Click here for full update information.
AuthorRSEM is mainly developed by Bo Li, who is a member of Deweylab.
RSEM is under the GNU General Public License
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 using Refseq set as reference
Simulation Data using Ensembl set as reference
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RSEM was developed with the help of Prof. Colin Dewey.
(last modified on Nov 22, 2013)