SAMMate protocols

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

Versioning


Add your version

Documentation


Maintainer


  • person_outline Dongxiao Zhu <>

Publication for SAMMate

SAMMate IN pipelines

 (6)
2017
PMCID: 5656618
PMID: 29070831
DOI: 10.1038/s41598-017-14342-8

[…] bcl2fastq2 v 2.17 program. tophat2 (2.0.7)43 was applied to align sequencing reads to the reference mouse genome (grcm38/mm10). the relative gene expression rpkm and read counts were estimated using sammate (2.7.4)44 and ensembl database (mus musculus.grcm38.82). protein coding genes with at least 2 rpkm on average in either condition were used to perform the differential gene expression […]

2014
PMCID: 4199489
PMID: 25330172
DOI: 10.1371/journal.pgen.1004662

[…] rna-seq short reads were mapped to the annotated genomes using tophat v2.0.11 [46]. for each sample, ∼2.0 gb of reads was mapped, representing ∼100× coverage of p. marneffei transcriptome. using sammate [47], the gene expression level was measured in fpkm (fragments per kilobase of exon per million fragments mapped) [48]. for each gene, expression levels associated with each of the four […]

2013
PMCID: 3699530
PMID: 23844188
DOI: 10.1371/journal.pone.0068352

[…] 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 […]

2013
PMCID: 3699530
PMID: 23844188
DOI: 10.1371/journal.pone.0068352

[…] 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 (reads assign […]

2013
PMCID: 3699530
PMID: 23844188
DOI: 10.1371/journal.pone.0068352

[…] software, was employed for gene and isoform quantification. for isoform quantification, we applied the method, raem (reads assign by expectation maximization), reported in [24] and implemented in sammate. the output results of sammate contain not only expression abundance level measured by rpkm (reads per kilobase of exon/transcript model per million mapped reads) [68], but also aligned read […]

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)

SAMMate reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SAMMate