Tin Nguyen
Guorong Xu
Nan Deng
Kristen Johnson
Zhiyu Zhao
Dongxiao Zhu

Getting help

If you have questions and comments, please joint  aSAMMate Group or email to

News and updates

5/11/2013 assemblySAM 1.1 is released.

11/10/2012 SAMMate 2.7.4 is released.

10/10/2012 SAMMate 2.7.3 is released.

8/9/2012 SAMMate 2.7.2 is released.

Introduction to SAMMate

SAMMate, a Graphical User Interface (GUI) RNA-seq analysis 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 three mRNA transcript quantification algorithms:

1. SASeq: A Selective and Adaptive Shrinkage Approach to Detect and Quantify the active transcript. Nguyen et al. arXiv:1208.3619

2. RAEM: Read Assignment via EM. Deng et al. Nucleic Acids Research, doi:10.1093/nar/gkr042.    

SAMMate manual



Feature list:

  • Estimating genomic feature abundance at isoform level
  • Calculating genomic feature abundance score at gene level
  • Generating signal map for peak detection
  • Generating wiggle files for visualization
  • Supported Fastq or Fasta format by calling Bowtie to align short reads to a reference genome
  • Generating alignment report
  • Customize gene annotation file
  • Customize chromosome name in output file
  • SAM/BAM format conversion
  • SAM/BAM file sorting
  • Supports edgeR to detect differentially expressed genes and isoforms.

Update news

Version 2.7

  • Supports edgeR to detect differentially expressed genes and isoforms.
  • Supported simultaneous multiple instances of SAMMate runs.
  • Users can export P-values to transcript expression file.
  • In the Work Space, added two group tabs to separate files into two groups.
  • In the Options dialogue, added R Options to configure R information

Frequently asked questions:

How many formats of gene annotation file can be supported by SAMMate?
SAMMate can support 4 gene annotation files in GTF, GFF3, refFlat and GeneBank format. Please use .ann as the extension of refFlat format and use .seq as the extension of GeneBank format.

Can SAMMate handle paired-end alignment results in the SAM/BAM format?
Yes, SAMMate can automatically detect if the inputting SAM/BAM files are paired-end or single-end.

Can SAMMate start with Fasta/Fastq file?
Sure. Since from version 2.6, SAMMate has integrated the Bowtie aligner to process Fasta/Fastq sequence files. For large Fasta/Fastq sequence files, the Mac and Linux version of SAMMate are recommended for efficiency and stability of the Bowtie aligner.

Can SAMMate process a batch of SAM/BAM files ?
Yes, SAMMate can process a batch of SAM/BAM files selected in "Work Space".

Can SAMMate process a pair of SAM/BAM and BED files ?
Yes, SAMMate can process the combination of SAM/BAM and BED file. When users input the SAM/BAM and BED files into the "Work Space", SAMMate can automatically process the SAM/BAM and BED files by the order of files, and the first SAM/BAM file and the first BED file would be the first combination, and the second SAM/BAM file plus the second BED file would be the second combination, and so on.

Can SAMMate support simultaneous multiple instances of SAMMate runs?
Yes. SAMMate 2.6.1 support this feature.

How do I find differentially expressed genes and transcripts with count-based?
You need to enable using edgeR in the Options dialogue, and then assign your sequence files into two different groups. SAMMate would automatically export the differential expressed genes and transcripts files using the counts of short reads that mapped in the genes and transcripts.

Where can I find the resulting files?
The resulting files reported by SAMMate would be generated in the directory of the inputted gene annotation file.