SAMMate specifications

Information


Unique identifier OMICS_01264
Name SAMMate
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNA-seq reads
Input format FASTQ
Output data Localized reads to each annotated gene or un-annotated transcriptional unit in the SAM format and assembled mRNA sequences in FASTA format
Output format SAM, FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Dongxiao Zhu <>

SAMMate article

SAMMate citation

2013
PMCID: 3699530

[…] saved in a sam format., based on the alignment results of all the samples, expression abundance estimation was conducted at both gene and isoform levels using ensembl astd database (version 60). sammate (http://sammate.sourceforge.net/), free graphical user interface (gui) software, was employed for gene and isoform quantification. for isoform quantification, we applied the method, raem […]

SAMMate institution(s)
Department of Computer Science, University of New Orleans, New Orleans, LA, USA; Tulane Cancer Center and Tulane Health Science Center, LA, USA; The Research Institute for Children, Children's Hospital, LA, USA
SAMMate funding source(s)
The Tulane Cancer Center Post-doctoral Matching Funds award; an NIH 1R21LM010137-01 grant; an NIH ARRA award (R01CA130752-02S1)

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