SAMMate protocols

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SAMMate specifications


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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  • person_outline Dongxiao Zhu <>

Publication for SAMMate

SAMMate in pipelines

PMCID: 5503541
PMID: 28415594
DOI: 10.18632/oncotarget.16417

[…] strong et al. []. briefly, alignment was carried out using novoalign [−o sam, paired-end, default options] against the ebv b95-8 genome, followed by ebv transcript quantification using the software sammate []., in our dataset, we have 25 ebv+ gc samples and 260 ebv− gc samples. to alleviate confounding effects during the process of comparing ebv+ and ebv− samples, we selected ebv− gc samples […]

PMCID: 5656618
PMID: 29070831
DOI: 10.1038/s41598-017-14342-8

[…] bcl2fastq2 v 2.17 program. tophat2 (2.0.7) 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) 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 analysis […]

PMCID: 4633283
PMID: 26536247
DOI: 10.1371/journal.pone.0141398

[…] of mapping were merged for each sample-replicate using samtools-0.1.19 []. finally, the merged new annotation file and merged accepted hits were applied to count the expression quantities using sammate-2.7.4 []., the inter-treatment comparisons were carried out using the edger []. global dispersion was applied and the significant expression changes were selected with minimum two-fold […]

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 . for each sample, ∼2.0 gb of reads was mapped, representing ∼100× coverage of p. marneffei transcriptome. using sammate , the gene expression level was measured in fpkm (fragments per kilobase of exon per million fragments mapped) . for each gene, expression levels associated with each of the four experimental […]

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 (, free graphical user interface (gui) software, was employed for gene and isoform quantification. for isoform quantification, we applied the method, raem […]

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SAMMate in publications

PMCID: 4893155
PMID: 27210754
DOI: 10.1016/j.celrep.2016.04.071

[…] to the mouse reference genome (mm9) using tophat (version 1.3.1.linux_x86_64,–coverage-search, -butterfly-search,–segment-mismatches 1,–segment-length 18) via the narwhal () automation software. sammate (; ) was used to detect and quantify transcripts. gene counts were calculated taking into account the reads mapped on exons or on exon-exon junctions. degs […]

PMCID: 3815106
PMID: 24223952
DOI: 10.1371/journal.pone.0079475

[…] in single read alignment mode. two previously published illumina sequencing datasets were also aligned to the c. jejuni nctc11168 genome for subsequent analysis and comparison with our dataset [,]., sammate with the edger statistical package was used to determine gene expression fold changes using the current genbank protein annotation information for c. jejuni nctc11168 [,].. in addition, […]

PMCID: 3784481
PMID: 24086132
DOI: 10.1371/journal.ppat.1003611

[…] tnfsf10 [a.k.a. trail]). interestingly, transcription factors (foxa1, en2, insm1, tbx21, [a.k.a t-bet], and tp73) were among the most strongly induced by mcmv infection., p<0.05 identified using sammate with edger., genes associated with genetic networks identified by ipa are shown in bold., p<0.05 identified using sammate with edger., genes associated with genetic networks identified […]

PMCID: 3865592
PMID: 24498620
DOI: 10.1002/mgg3.23

[…] on leukemic cells. the rna splicing maps were obtained by using tophat (trapnell et al. ), a splice junction mapper algorithm, and the whole-gene expression profile analysis was performed by sammate (xu et al. ). when possible we confirmed the novel mrna splicing by reverse transcription-polymerase chain reaction (rt-pcr)., to test the ability of splicefinder to identify splicing […]

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

[…] viewer (igv) (version 1.5), free software available from to visualize the read coverage signal map of control and ipf samples in igv, the wig files generated from sammate were converted to the compatible igv format using the “tile” function of igvtools. the igvtools were embedded in the igv software., the analysis of differential expression of transcripts […]

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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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