RSEM (RNA-Seq by Expectation-Maximization)


Oct 3, 2016   RSEM v1.3.0 is online now. Added Prior-Enhanced RSEM (pRSEM) as a submodule. Introduced `--strandedness <none|forward|reverse>` option, `--strand-specific` and `--forward-prob` are deprecated (but still supported). Revised documentation for `rsem-plot-model`, maked it clear that in alignment statistics, isoform-level (instead of genome-level) multi-mapping reads are shown. Significantly improved the output information of `rsem-sam-validator`: if indels/clippings/skips are detected in alignments or alignments exceed transcript boundaries, `rsem-sam-validator` will report them instead of telling you the input is valid. Updated the warning message to ask users to make sure that they align their reads agains a set of transcripts instead of genome when RSEM finds less sequences in the BAM file than RSEM's indices.

Jun 4, 2016   RSEM v1.2.31 is online now. Rewrote 'rsem-gff3-to-gtf' to handle a more general set of GFF3 files. Added safety checks to make sure poly(A) tails are not added to the reference when '--star' is set.

Apr 24, 2016   Notification: Since RSEM v1.2.27, '--sort-bam-by-coordinate' needs to be set if sorted BAMs are required.

Apr 20, 2016   RSEM v1.2.30 is online now. Fixed a bug that can cause SAMtools sort to fail. Improved the appearance of warning messages: for the same type of warning messages, only show the first 50 messages and then provide the total number of such warnings.

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Source Code



Bo Li and Colin Dewey designed the RSEM algorithm. Bo Li implemented the RSEM software. Peng Liu contributed the STAR aligner options.


RSEM is under the GNU General Public License

Prebuilt RSEM Indices (RSEM v1.1.17) 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

Reference annotations and Simulation Data used in the paper

RefSeq and Ensembl annotation GTF files used in the paper

Simulation Data using Refseq set as reference

Simulation Data using Ensembl set as reference

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(last modified on Oct 3, 2016)