RSEM (RNA-Seq by Expectation-Maximization)


Updates

Sept 4, 2014   RSEM v1.2.17 is online now. Added error detection for cases such as a read's two mates having different names or a read is both alignable and unalignable.

Aug 18, 2014   RSEM v1.2.16 is online now. Corrected a typo in 'rsem-generate-data-matrix', this script extracts 'expected_count' column instead of 'TPM' column.

Jun 16, 2014   RSEM v1.2.15 is online now. Allowed for a subset of reference sequences to be declared in an input SAM/BAM file. For any transcript not declared in the SAM/BAM file, its PME estimates and credibility intervals are set to zero. Added advanced options for customizing Gibbs sampler and credibility interval calculation behaviors. Splitted options in 'rsem-calculate-expression' into basic and advanced options.

Click here for full update information.

Author

RSEM is mainly developed by Bo Li, who was a member of Deweylab.

License

RSEM is under the GNU General Public License

Source Code

Documentation

README

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

Simulation Data

Simulation Data using Refseq set as reference

Simulation Data using Ensembl set as reference

Google Users and Announce Groups

Google Groups
Subscribe to RSEM Announce
Email:
Visit this group
Google Groups
Subscribe to RSEM Users
Email:
Visit this group

Acknowledgements

RSEM was developed with the help of Prof. Colin Dewey.


(last modified on Sept 4, 2014)