Updates
Feb 14, 2020 RSEM v1.3.3 is online now. Added HISAT2 option (--hisat2-hca) using Human Cell Atlas SMART-Seq2 pipeline parameters. Fixed a bug in RSEM simulator.
Apr 6, 2019 RSEM v1.3.2 is online now. Prevented RSEM from crashing when there is 0 aligned reads. Outputted theta and model files even there is no aligned reads.
Jun 27, 2018 RSEM v1.3.1 is online now. Added `--gff3-genes-as-transcripts` option for `rsem-prepare-reference`. This option will allow RSEM to treat genes as transcripts.
Click here for full update information.
Source Code
Documentation
Authors
Bo Li and Colin Dewey designed the RSEM algorithm. Bo Li implemented the RSEM software. Peng Liu contributed the STAR aligner options and pRSEM.
License
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
Google Users and Announce Groups
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(last modified on Feb 14, 2020)