Introduction
SAMMate is an open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.
assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA transcript sequences.
Download Simulation Data and Scripts for SPATA
SAMMate, a GUI RNA-seq quantification pipeline, allows biomedical researchers to quickly process fasta/fastq and SAM/BAM files, and is compatible with both single-end and paired-end sequencing technologies. SAMMate implements the following two transcript quantification algorithms developed in our research group:
Download Simulation Data and Scripts for SASeq
Pipeline
assemblySAM
==========>==========================>=============================>>
![](SWimages/contig_small.jpg)
![](SWimages/sammate_small.jpg)
=============>==================>>
SAMMate
Contributors
SAMMate is an open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.
assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA transcript sequences.
- The inputs are RNA-seq reads in the .fastq format.
- Two kinds of outputs: (1). Localized reads to each annotated gene or un-annotated transcriptional unit in the SAM format. (2). Assembled mRNA sequences in .fasta format.
Download Simulation Data and Scripts for SPATA
SAMMate, a GUI RNA-seq quantification pipeline, allows biomedical researchers to quickly process fasta/fastq and SAM/BAM files, and is compatible with both single-end and paired-end sequencing technologies. SAMMate implements the following two transcript quantification algorithms developed in our research group:
- Read Assignment via Expectation Maximiation (RAEM) (Deng et al. Nucleic Acids Research doi: 10.1093/nar/gkr042).
- Selective and Adaptive Shrinkage Approach to Detect and Quantify Active Transcripts (SASeq). (Nguyen et al. arXiv:1208.3619)
Download Simulation Data and Scripts for SASeq
Pipeline
assemblySAM
==========>==========================>=============================>>
![](SWimages/fasta_small.jpg)
![](SWimages/localize_small.jpg)
![](SWimages/sam_small.jpg)
![](SWimages/assembly_small.jpg)
![](SWimages/contig_small.jpg)
![](SWimages/quantify_small.jpg)
![](SWimages/sammate_small.jpg)
=============>==================>>
SAMMate
Contributors
- Dongxiao Zhu: Associate Professor, Department of Computer Science, Wayne State University (Principal Investigator), email: dzhu@wayne.edu, website: http://www.cs.wayne.edu/dzhu/
- Nan Deng: PhD student, Department of Computer Science, Wayne State University
- Tin Nguyen (previous contributor), PhD student, Department of Computer Science, Wayne State University
- Guorong Xu (previous contributor, now at
Baylor Dallas)
- Kristen Johnson (previous contributor, now
at Purdue)
- Zhiyu Zhao (previous contributor, now at UT
Southwestern Medical Center)