BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data Long Description (required)
By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required (available below). http://cbil.upenn.edu/BEERS/
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
Every sub-attribute is selected Not all sub-attributes are selectedFill Clear Expand Collapse Reset
Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
Can't Find the Attribute You Are Looking For? If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab .
Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 21775302 ],
Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA ,
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). ,
Bioinformatics ,
09-15-2011 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=21775302, Primary Citation
[Pubmed ID: 35076116 ],
Huang R, Balu AR, Molitoris KH, White JP, Robling AG, Ayturk UM, Baht GS ,
The role of Meteorin-like in skeletal development and bone fracture healing. ,
J Orthop Res ,
11-01-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35076116, , Application
[Pubmed ID: 35422952 ],
Donnenfield JI, Karamchedu NP, Fleming BC, Molino J, Proffen BL, Murray MM ,
Articular cartilage and synovium may be important sources of post-surgical synovial fluid inflammatory mediators. ,
Am J Transl Res ,
03-15-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35422952, , Application